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source: issm/trunk-jpl/src/m/classes/model.m@ 25118

Last change on this file since 25118 was 25118, checked in by Eric.Larour, 5 years ago
CHG: significant changes to the organization of slr -> new solidearth class that encompasses all of the slr fields.
File size: 70.6 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;
[22958]	41	levelset = 0;
[18757]	42	calving = 0;
[23652]	43	frontalforcings = 0;
[22958]	44	love = 0;
	45	gia = 0;
[21260]	46	esa = 0;
[22958]	47
[13692]	48	autodiff = 0;
	49	inversion = 0;
	50	qmu = 0;
[22955]	51	amr = 0;
[13692]	52	results = 0;
[16388]	53	outputdefinition = 0;
[13692]	54	radaroverlay = 0;
	55	miscellaneous = 0;
	56	private = 0;
[9778]	57
[13692]	58	%}}}
	59	end
	60	methods (Static)
	61	function md = loadobj(md) % {{{
	62	% This function is directly called by matlab when a model object is
	63	% loaded. If the input is a struct it is an old version of model and
	64	% old fields must be recovered (make sure they are in the deprecated
	65	% model properties)
[8926]	66
[13692]	67	if verLessThan('matlab','7.9'),
	68	disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
	69	disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
[8952]	70
[13692]	71	% This is a Matlab bug: all the fields of md have their default value
	72	% Example of error message:
	73	% Warning: Error loading an object of class 'model':
	74	% Undefined function or method 'exist' for input arguments of type 'cell'
	75	%
	76	% This has been fixed in MATLAB 7.9 (R2009b) and later versions
	77	end
[8952]	78
[13692]	79	if isstruct(md)
	80	disp('Recovering model object from a previous version');
	81	md = structtomodel(model,md);
	82	end
[13239]	83
[13692]	84	%2012 August 4th
	85	if isa(md.materials,'materials'),
	86	disp('Recovering old materials');
	87	if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
[13718]	88	md.materials=matice(md.materials);
	89	else
[13692]	90	md.materials=matdamageice(md.materials);
	91	end
	92	end
[14559]	93	%2013 April 12
[15771]	94	if numel(md.stressbalance.loadingforce==1)
	95	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14559]	96	end
[14618]	97	%2013 April 17
	98	if isa(md.hydrology,'hydrology'),
	99	disp('Recovering old hydrology class');
	100	md.hydrology=hydrologyshreve(md.materials);
	101	end
[16356]	102	%2013 October 9
	103	if ~isa(md.damage,'damage'),
	104	md.damage=damage();
	105	md.damage.D=zeros(md.mesh.numberofvertices,1);
	106	md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
	107	end
[16822]	108	%2013 November 18
	109	if ~isa(md.outputdefinition,'outputdefinition'),
	110	md.outputdefinition=outputdefinition();
	111	end
[17558]	112	%2014 March 26th
	113	if isa(md.mesh,'mesh'),
[17566]	114	disp('Recovering old mesh class');
	115	if isprop(md.mesh,'dimension'),
	116	if md.mesh.dimension==2,
	117	md.mesh=mesh2d(md.mesh);
	118	else
	119	md.mesh=mesh3dprisms(md.mesh);
	120	end
[17558]	121	else
[17566]	122	md.mesh=mesh2dvertical(md.mesh);
[17558]	123	end
	124	end
[18775]	125	%2014 November 12
[21702]	126	if isa(md.calving,'double'); md.calving=calving(); end
[20059]	127	%2016 February 3
[25118]	128	if isa(md.slr,'double'); md.solidearth=solidearth(); end
[21260]	129	%2016 October 11
[21702]	130	if isa(md.esa,'double'); md.esa=esa(); end
[21545]	131	%2017 February 10th
[23434]	132	if isa(md.settings,'settings'), %this 'isa' verification: 2018 October 24th
	133	if md.settings.solver_residue_threshold==0,
	134	md.settings.solver_residue_threshold = 1e-6;
	135	end
[21545]	136	end
[21667]	137	%2017 April 10th
[25066]	138	if isa(md.gia,'gia'), md.gia=giamme(); end
[21702]	139	%2017 May 4th
	140	if isa(md.amr,'double'); md.amr=amr(); end
[22019]	141	%2017 Aug 29th
[22040]	142	if isa(md.love,'double'); md.love=fourierlove(); end
[22194]	143	%2017 Oct 26th
	144	if isa(md.calving,'calvingdev')
	145	disp('Warning: calvingdev is now calvingvonmises');
	146	md.calving=calvingvonmises(md.calving);
	147	end
[22955]	148	%2017 Dec 21st (needs to be here)
	149	if isempty(md.settings)
	150	disp('Warning: md.settings had to be reset, make sure to adjust md.settings.output_frequency and other fields');
	151	md.settings = issmsettings();
	152	end
[23503]	153	%2018 Dec 1st
	154	if md.settings.sb_coupling_frequency==0
	155	md.settings.sb_coupling_frequency=1;
	156	end
[23652]	157	%2019 Jan..
	158	if isa(md.frontalforcings,'double');
[24476]	159	if(isprop('meltingrate',md.calving) & ~isnan(md.calving.meltingrate))
[23652]	160	disp('Warning: md.calving.meltingrate is now in md.frontalforcings');
	161	end
	162	md.frontalforcings=frontalforcings(md.calving);
	163	end
[23758]	164	%2019 Feb 26
	165	if isa(md.settings.results_on_nodes,'double')
	166	if md.settings.results_on_nodes == 0
	167	md.settings.results_on_nodes = {};
	168	else
	169	md.settings.results_on_nodes = {'all'};
	170	end
	171	end
[23814]	172	%2019 Mar 28
[23984]	173	if isa(md.smb,'SMBcomponents') \| isa(md.smb,'SMBmeltcomponents') \| isa(md.smb,'SMBforcing') \| isa(md.smb,'SMBgemb')
	174	if isa(md.smb.isclimatology,'double')
	175	if prod(size(md.smb.isclimatology)) ~= 1
	176	md.smb.isclimatology = 0;
	177	end
[23814]	178	end
	179	end
[24474]	180	%2019 Dec 16
[24510]	181	if isa(md.dsl,'double') \| isempty(md.dsl.compute_fingerprints)
[24474]	182	md.dsl=dsl();
	183	end
[24738]	184	%2020 April 24
	185	if isa(md.smb,'SMBgemb')
	186	if isa(md.smb.isconstrainsurfaceT,'double')
	187	if prod(size(md.smb.isconstrainsurfaceT)) ~= 1
	188	md.smb.isconstrainsurfaceT = 0;
	189	end
	190	end
	191	end
[13692]	192	end% }}}
	193	end
	194	methods
	195	function md = model(varargin) % {{{
[8926]	196
[13692]	197	switch nargin
	198	case 0
	199	md=setdefaultparameters(md);
[18492]	200	case 1
[19087]	201	error('model constructor not supported yet');
[18503]	202
[13692]	203	otherwise
	204	error('model constructor error message: 0 of 1 argument only in input.');
	205	end
	206	end
	207	%}}}
	208	function md = checkmessage(md,string) % {{{
	209	if(nargout~=1) error('wrong usage, model must be an output'); end
	210	disp(['model not consistent: ' string]);
	211	md.private.isconsistent=false;
	212	end
	213	%}}}
	214	function md = collapse(md)% {{{
	215	%COLLAPSE - collapses a 3d mesh into a 2d mesh
	216	%
	217	% This routine collapses a 3d model into a 2d model
	218	% and collapses all the fileds of the 3d model by
	219	% taking their depth-averaged values
	220	%
	221	% Usage:
	222	% md=collapse(md)
	223	%
	224	% See also: EXTRUDE, MODELEXTRACT
[13005]	225
[13692]	226	%Check that the model is really a 3d model
[17687]	227	if ~strcmp(md.mesh.elementtype(),'Penta'),
[13692]	228	error('collapse error message: only 3d mesh can be collapsed')
	229	end
[13005]	230
[17724]	231	%Start with changing all the fields from the 3d mesh
[13005]	232
[21827]	233	%dealing with the friction law
[13692]	234	%drag is limited to nodes that are on the bedrock.
[18775]	235	if isa(md.friction,'friction'),
	236	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	237	md.friction.p=project2d(md,md.friction.p,1);
	238	md.friction.q=project2d(md,md.friction.q,1);
[21819]	239	elseif isa(md.friction,'frictioncoulomb'),
	240	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	241	md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1);
	242	md.friction.p=project2d(md,md.friction.p,1);
	243	md.friction.q=project2d(md,md.friction.q,1);
[18775]	244	elseif isa(md.friction,'frictionhydro'),
	245	md.friction.q=project2d(md,md.friction.q,1);
	246	md.friction.C=project2d(md,md.friction.C,1);
	247	md.friction.As=project2d(md,md.friction.As,1);
[18798]	248	md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
[18775]	249	elseif isa(md.friction,'frictionwaterlayer'),
	250	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	251	md.friction.p=project2d(md,md.friction.p,1);
	252	md.friction.q=project2d(md,md.friction.q,1);
	253	md.friction.water_layer=project2d(md,md.friction.water_layer,1);
	254	elseif isa(md.friction,'frictionweertman'),
	255	md.friction.C=project2d(md,md.friction.C,1);
	256	md.friction.m=project2d(md,md.friction.m,1);
[19720]	257	elseif isa(md.friction,'frictionweertmantemp'),
	258	md.friction.C=project2d(md,md.friction.C,1);
	259	md.friction.m=project2d(md,md.friction.m,1);
	260	else
	261	disp('friction type not supported');
[21827]	262	end
[13005]	263
[13692]	264	%observations
	265	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
	266	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
	267	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
[24465]	268	if ~isnan(md.inversion.thickness_obs), md.inversion.thickness_obs=project2d(md,md.inversion.thickness_obs,md.mesh.numberoflayers); end;
[13692]	269	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
	270	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
	271	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
[19527]	272	if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
	273	md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
	274	elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
	275	md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
[13692]	276	end;
[13005]	277
[13692]	278	%results
	279	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
	280	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
	281	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
	282	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
[18578]	283	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[18506]	284	if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
[18578]	285	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
	286	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
	287	if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
[21417]	288	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
	289	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
[21530]	290	%giaivins
[25074]	291	if isa(md.gia,'giaivins'),
	292	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
	293	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
	294	end
[15021]	295
[13692]	296	%elementstype
	297	if ~isnan(md.flowequation.element_equation)
	298	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
	299	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]	300	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
	301	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
	302	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]	303	end
[13005]	304
[13692]	305	%boundary conditions
[15771]	306	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
	307	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
	308	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
	309	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
	310	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[24536]	311	if numel(md.masstransport.spcthickness)>1 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers); end
[21544]	312	if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
[21417]	313	if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
[13692]	314	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]	315
[18506]	316	% Hydrologydc variables
	317	if isa(md.hydrology,'hydrologydc');
	318	md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
	319	md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
	320	md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
	321	md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
	322	if(md.hydrology.isefficientlayer==1)
	323	md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
[21808]	324	end
	325	end
[18506]	326
[13692]	327	%materials
	328	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
	329	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]	330
	331	%damage:
[17940]	332	if md.damage.isdamage,
	333	md.damage.D=DepthAverage(md,md.damage.D);
	334	end
[13005]	335
[13692]	336	%special for thermal modeling:
[18378]	337	if ~isnan(md.basalforcings.groundedice_melting_rate),
	338	md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
	339	end
[21417]	340	if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
[18378]	341	md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
	342	end
[13692]	343	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]	344
[21417]	345	if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
	346	md.calving.coeff=project2d(md,md.calving.coeff,1);
	347	end
[23652]	348	if isprop(md.frontalforcings,'meltingrate') & ~isnan(md.frontalforcings.meltingrate),
	349	md.frontalforcings.meltingrate=project2d(md,md.frontalforcings.meltingrate,1);
[21417]	350	end
	351
[13692]	352	%update of connectivity matrix
	353	md.mesh.average_vertex_connectivity=25;
[13005]	354
[13692]	355	%Collapse the mesh
	356	nodes2d=md.mesh.numberofvertices2d;
	357	elements2d=md.mesh.numberofelements2d;
[13005]	358
[13692]	359	%parameters
	360	md.geometry.surface=project2d(md,md.geometry.surface,1);
	361	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
[17590]	362	md.geometry.base=project2d(md,md.geometry.base,1);
[18480]	363	if ~isnan(md.geometry.bed),
	364	md.geometry.bed=project2d(md,md.geometry.bed,1);
	365	end
[17991]	366
[24861]	367	if ~isnan(md.mask.ocean_levelset),
	368	md.mask.ocean_levelset=project2d(md,md.mask.ocean_levelset,1);
[18378]	369	end
	370	if ~isnan(md.mask.ice_levelset),
	371	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
	372	end
[13005]	373
[22955]	374	%lat long
	375	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
	376	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
	377
[21808]	378	%outputdefinitions
	379	for i=1:length(md.outputdefinition.definitions)
	380	if isobject(md.outputdefinition.definitions{i})
	381	%get subfields
	382	solutionsubfields=fields(md.outputdefinition.definitions{i});
	383	for j=1:length(solutionsubfields),
	384	field=md.outputdefinition.definitions{i}.(solutionsubfields{j});
	385	if length(field)==md.mesh.numberofvertices \| length(field)==md.mesh.numberofelements,
	386	md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1);
	387	end
	388	end
	389	end
	390	end
	391
[13692]	392	%Initialize with the 2d mesh
[17724]	393	mesh=mesh2d();
	394	mesh.x=md.mesh.x2d;
	395	mesh.y=md.mesh.y2d;
	396	mesh.numberofvertices=md.mesh.numberofvertices2d;
	397	mesh.numberofelements=md.mesh.numberofelements2d;
	398	mesh.elements=md.mesh.elements2d;
[21499]	399	if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end
	400	if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end
	401	mesh.epsg=md.mesh.epsg;
[22324]	402	if numel(md.mesh.scale_factor)==md.mesh.numberofvertices, mesh.scale_factor=project2d(md,md.mesh.scale_factor,1); end
[17991]	403	if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
	404	if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
[17724]	405	md.mesh=mesh;
[18738]	406	md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
	407	md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
[19955]	408	md.mesh.segments=contourenvelope(md.mesh);
[13005]	409
[13692]	410	end % }}}
[22955]	411	function md2 = extract(md,area,varargin) % {{{
[13692]	412	%extract - extract a model according to an Argus contour or flag list
	413	%
	414	% This routine extracts a submodel from a bigger model with respect to a given contour
	415	% md must be followed by the corresponding exp file or flags list
	416	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
	417	% If user wants every element outside the domain to be
[15564]	418	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]	419	% an empty string '' will be considered as an empty domain
	420	% a string 'all' will be considered as the entire domain
	421	%
	422	% Usage:
	423	% md2=extract(md,area);
	424	%
	425	% Examples:
	426	% md2=extract(md,'Domain.exp');
	427	%
	428	% See also: EXTRUDE, COLLAPSE
[13005]	429
[13692]	430	%copy model
	431	md1=md;
[13005]	432
[22955]	433	%recover optoins:
	434	options=pairoptions(varargin{:});
	435
[13692]	436	%some checks
[22955]	437	if ((nargin<2) \| (nargout~=1)),
[13692]	438	help extract
	439	error('extract error message: bad usage');
	440	end
[13005]	441
[13692]	442	%get elements that are inside area
	443	flag_elem=FlagElements(md1,area);
	444	if ~any(flag_elem),
	445	error('extracted model is empty');
	446	end
[13005]	447
[13692]	448	%kick out all elements with 3 dirichlets
[22955]	449	if getfieldvalue(options,'spccheck',1)
	450	spc_elem=find(~flag_elem);
	451	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
	452	flag=ones(md1.mesh.numberofvertices,1);
	453	flag(spc_node)=0;
	454	pos=find(sum(flag(md1.mesh.elements),2)==0);
	455	flag_elem(pos)=0;
	456	end
[13005]	457
[13692]	458	%extracted elements and nodes lists
	459	pos_elem=find(flag_elem);
	460	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]	461
[13692]	462	%keep track of some fields
	463	numberofvertices1=md1.mesh.numberofvertices;
	464	numberofelements1=md1.mesh.numberofelements;
	465	numberofvertices2=length(pos_node);
	466	numberofelements2=length(pos_elem);
	467	flag_node=zeros(numberofvertices1,1);
	468	flag_node(pos_node)=1;
[13005]	469
[13692]	470	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
	471	Pelem=zeros(numberofelements1,1);
	472	Pelem(pos_elem)=[1:numberofelements2]';
	473	Pnode=zeros(numberofvertices1,1);
	474	Pnode(pos_node)=[1:numberofvertices2]';
[13005]	475
[13857]	476	%renumber the elements (some nodes won't exist anymore)
[13692]	477	elements_1=md1.mesh.elements;
	478	elements_2=elements_1(pos_elem,:);
	479	elements_2(:,1)=Pnode(elements_2(:,1));
	480	elements_2(:,2)=Pnode(elements_2(:,2));
	481	elements_2(:,3)=Pnode(elements_2(:,3));
[17558]	482	if isa(md1.mesh,'mesh3dprisms'),
[13692]	483	elements_2(:,4)=Pnode(elements_2(:,4));
	484	elements_2(:,5)=Pnode(elements_2(:,5));
	485	elements_2(:,6)=Pnode(elements_2(:,6));
	486	end
[13005]	487
[13857]	488	%OK, now create the new model!
[13005]	489
[13857]	490	%take every field from model
[13692]	491	md2=md1;
[13005]	492
[13692]	493	%automatically modify fields
[13005]	494
[13692]	495	%loop over model fields
	496	model_fields=fields(md1);
	497	for i=1:length(model_fields),
	498	%get field
	499	field=md1.(model_fields{i});
	500	fieldsize=size(field);
	501	if isobject(field), %recursive call
	502	object_fields=fields(md1.(model_fields{i}));
	503	for j=1:length(object_fields),
	504	%get field
	505	field=md1.(model_fields{i}).(object_fields{j});
	506	fieldsize=size(field);
	507	%size = number of nodes * n
	508	if fieldsize(1)==numberofvertices1
	509	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
	510	elseif (fieldsize(1)==numberofvertices1+1)
	511	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]	512	%size = number of elements * n
[13692]	513	elseif fieldsize(1)==numberofelements1
	514	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
[21428]	515	elseif (fieldsize(1)==numberofelements1+1)
	516	md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
[13692]	517	end
	518	end
	519	else
	520	%size = number of nodes * n
	521	if fieldsize(1)==numberofvertices1
	522	md2.(model_fields{i})=field(pos_node,:);
	523	elseif (fieldsize(1)==numberofvertices1+1)
	524	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]	525	%size = number of elements * n
[13692]	526	elseif fieldsize(1)==numberofelements1
	527	md2.(model_fields{i})=field(pos_elem,:);
[21428]	528	elseif (fieldsize(1)==numberofelements1+1)
	529	md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
[13692]	530	end
	531	end
	532	end
[13005]	533
[13692]	534	%modify some specific fields
[13005]	535
[13692]	536	%Mesh
	537	md2.mesh.numberofelements=numberofelements2;
	538	md2.mesh.numberofvertices=numberofvertices2;
	539	md2.mesh.elements=elements_2;
[13005]	540
[13692]	541	%mesh.uppervertex mesh.lowervertex
[17558]	542	if isa(md1.mesh,'mesh3dprisms'),
[13692]	543	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
	544	pos=find(~isnan(md2.mesh.uppervertex));
	545	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]	546
[13692]	547	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
	548	pos=find(~isnan(md2.mesh.lowervertex));
	549	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]	550
[13692]	551	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
	552	pos=find(~isnan(md2.mesh.upperelements));
	553	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]	554
[13692]	555	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
	556	pos=find(~isnan(md2.mesh.lowerelements));
	557	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
	558	end
[13005]	559
[13692]	560	%Initial 2d mesh
[17558]	561	if isa(md1.mesh,'mesh3dprisms'),
[13692]	562	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
	563	pos_elem_2d=find(flag_elem_2d);
	564	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
	565	pos_node_2d=find(flag_node_2d);
[13005]	566
[13692]	567	md2.mesh.numberofelements2d=length(pos_elem_2d);
	568	md2.mesh.numberofvertices2d=length(pos_node_2d);
	569	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
	570	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
	571	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
	572	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]	573
[13692]	574	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
	575	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
	576	end
[13005]	577
[13692]	578	%Edges
[17686]	579	if(dimension(md.mesh)==2),
[17563]	580	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
	581	%renumber first two columns
	582	pos=find(md2.mesh.edges(:,4)~=-1);
	583	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
	584	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
	585	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
	586	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
	587	%remove edges when the 2 vertices are not in the domain.
	588	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
	589	%Replace all zeros by -1 in the last two columns
	590	pos=find(md2.mesh.edges(:,3)==0);
	591	md2.mesh.edges(pos,3)=-1;
	592	pos=find(md2.mesh.edges(:,4)==0);
	593	md2.mesh.edges(pos,4)=-1;
	594	%Invert -1 on the third column with last column (Also invert first two columns!!)
	595	pos=find(md2.mesh.edges(:,3)==-1);
	596	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
	597	md2.mesh.edges(pos,4)=-1;
	598	values=md2.mesh.edges(pos,2);
	599	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
	600	md2.mesh.edges(pos,1)=values;
	601	%Finally remove edges that do not belong to any element
	602	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
	603	md2.mesh.edges(pos,:)=[];
	604	end
[13692]	605	end
[13005]	606
[13692]	607	%Penalties
[15771]	608	if ~isnan(md2.stressbalance.vertex_pairing),
	609	for i=1:size(md1.stressbalance.vertex_pairing,1);
	610	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]	611	end
[15771]	612	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]	613	end
[15767]	614	if ~isnan(md2.masstransport.vertex_pairing),
	615	for i=1:size(md1.masstransport.vertex_pairing,1);
	616	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]	617	end
[15767]	618	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]	619	end
[13005]	620
[13692]	621	%recreate segments
[20322]	622	if isa(md1.mesh,'mesh2d') \| isa(md1.mesh','mesh3dsurface'),
[13692]	623	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	624	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
[19957]	625	md2.mesh.segments=contourenvelope(md2.mesh);
[13692]	626	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
	627	else
	628	%First do the connectivity for the contourenvelope in 2d
	629	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
	630	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
[19957]	631	segments=contourenvelope(md2.mesh);
[17565]	632	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
[13692]	633	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
	634	%Then do it for 3d as usual
	635	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	636	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	637	end
[13005]	638
[13692]	639	%Boundary conditions: Dirichlets on new boundary
	640	%Catch the elements that have not been extracted
	641	orphans_elem=find(~flag_elem);
	642	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
	643	%Figure out which node are on the boundary between md2 and md1
	644	nodestoflag1=intersect(orphans_node,pos_node);
	645	nodestoflag2=Pnode(nodestoflag1);
[23771]	646	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>1 & numel(md1.stressbalance.spcvz)>1,
[13692]	647	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]	648	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
	649	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]	650	else
[15771]	651	md2.stressbalance.spcvx(nodestoflag2)=NaN;
	652	md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]	653	disp(' ')
	654	disp('!! extract warning: spc values should be checked !!')
	655	disp(' ')
	656	end
	657	%put 0 for vz
[15771]	658	md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]	659	end
	660	if ~isnan(md1.thermal.spctemperature),
	661	md2.thermal.spctemperature(nodestoflag2,1)=1;
	662	end
[13005]	663
[13692]	664	%Results fields
	665	if isstruct(md1.results),
	666	md2.results=struct();
	667	solutionfields=fields(md1.results);
	668	for i=1:length(solutionfields),
[14230]	669	if isstruct(md1.results.(solutionfields{i}))
	670	%get subfields
[24134]	671	% loop over time steps
	672	for p=1:length(md1.results.(solutionfields{i}))
	673	current = md1.results.(solutionfields{i})(p);
	674	solutionsubfields=fields(current);
	675	for j=1:length(solutionsubfields),
	676	field=md1.results.(solutionfields{i})(p).(solutionsubfields{j});
[14230]	677	if length(field)==numberofvertices1,
[24134]	678	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_node);
[14230]	679	elseif length(field)==numberofelements1,
[24134]	680	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_elem);
[14230]	681	else
[24134]	682	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field;
[14230]	683	end
[24134]	684	end
[14230]	685	end
	686	else
	687	field=md1.results.(solutionfields{i});
[13692]	688	if length(field)==numberofvertices1,
[14230]	689	md2.results.(solutionfields{i})=field(pos_node);
[13692]	690	elseif length(field)==numberofelements1,
[14230]	691	md2.results.(solutionfields{i})=field(pos_elem);
[13692]	692	else
[14230]	693	md2.results.(solutionfields{i})=field;
[13692]	694	end
	695	end
	696	end
	697	end
[13005]	698
[21808]	699	%OutputDefinitions fields
	700	for i=1:length(md1.outputdefinition.definitions),
	701	if isobject(md1.outputdefinition.definitions{i})
	702	%get subfields
	703	solutionsubfields=fields(md1.outputdefinition.definitions{i});
	704	for j=1:length(solutionsubfields),
	705	field=md1.outputdefinition.definitions{i}.(solutionsubfields{j});
	706	if length(field)==numberofvertices1,
	707	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node);
	708	elseif length(field)==numberofelements1,
	709	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem);
	710	end
	711	end
	712	end
	713	end
	714
[13692]	715	%Keep track of pos_node and pos_elem
	716	md2.mesh.extractedvertices=pos_node;
	717	md2.mesh.extractedelements=pos_elem;
	718	end % }}}
	719	function md = extrude(md,varargin) % {{{
	720	%EXTRUDE - vertically extrude a 2d mesh
	721	%
	722	% vertically extrude a 2d mesh and create corresponding 3d mesh.
	723	% The vertical distribution can:
	724	% - follow a polynomial law
	725	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
	726	% - be discribed by a list of coefficients (between 0 and 1)
	727	%
	728	%
	729	% Usage:
	730	% md=extrude(md,numlayers,extrusionexponent);
	731	% md=extrude(md,numlayers,lowerexponent,upperexponent);
	732	% md=extrude(md,listofcoefficients);
	733	%
	734	% Example:
[18216]	735	% md=extrude(md,15,1.3);
	736	% md=extrude(md,15,1.3,1.2);
[13692]	737	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
	738	%
	739	% See also: MODELEXTRACT, COLLAPSE
[13005]	740
[13692]	741	%some checks on list of arguments
	742	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
	743	help extrude;
	744	error('extrude error message');
	745	end
[24511]	746	if numel(md.geometry.base)~=md.mesh.numberofvertices \|\| numel(md.geometry.surface)~=md.mesh.numberofvertices
	747	error('model has not been parameterized yet: base and/or surface not set');
	748	end
[13005]	749
[13692]	750	%Extrude the mesh
	751	if nargin==2, %list of coefficients
	752	clist=varargin{1};
	753	if any(clist<0) \| any(clist>1),
	754	error('extrusioncoefficients must be between 0 and 1');
	755	end
	756	extrusionlist=sort(unique([clist(:);0;1]));
	757	numlayers=length(extrusionlist);
	758	elseif nargin==3, %one polynomial law
	759	if varargin{2}<=0,
	760	help extrude;
	761	error('extrusionexponent must be >=0');
	762	end
	763	numlayers=varargin{1};
	764	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
	765	elseif nargin==4, %two polynomial laws
	766	numlayers=varargin{1};
	767	lowerexp=varargin{2};
	768	upperexp=varargin{3};
[13005]	769
[13692]	770	if varargin{2}<=0 \| varargin{3}<=0,
	771	help extrude;
	772	error('lower and upper extrusionexponents must be >=0');
	773	end
[13005]	774
[13692]	775	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
	776	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
	777	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]	778
[13692]	779	end
[13005]	780
[13692]	781	if numlayers<2,
	782	error('number of layers should be at least 2');
	783	end
[17686]	784	if strcmp(md.mesh.domaintype(),'3D')
[13692]	785	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
	786	end
[13005]	787
[13692]	788	%Initialize with the 2d mesh
[17558]	789	mesh2d = md.mesh;
	790	md.mesh=mesh3dprisms();
	791	md.mesh.x = mesh2d.x;
	792	md.mesh.y = mesh2d.y;
	793	md.mesh.elements = mesh2d.elements;
	794	md.mesh.numberofelements = mesh2d.numberofelements;
	795	md.mesh.numberofvertices = mesh2d.numberofvertices;
	796
	797	md.mesh.lat = mesh2d.lat;
	798	md.mesh.long = mesh2d.long;
[18558]	799	md.mesh.epsg = mesh2d.epsg;
[22324]	800	md.mesh.scale_factor = mesh2d.scale_factor;
[17558]	801
	802	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
	803	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
	804	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
	805	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
	806
	807	md.mesh.extractedvertices = mesh2d.extractedvertices;
	808	md.mesh.extractedelements = mesh2d.extractedelements;
	809
[13692]	810	x3d=[];
	811	y3d=[];
	812	z3d=[]; %the lower node is on the bed
	813	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
[17590]	814	bed3d=md.geometry.base;
[13005]	815
[13692]	816	%Create the new layers
	817	for i=1:numlayers,
	818	x3d=[x3d; md.mesh.x];
	819	y3d=[y3d; md.mesh.y];
	820	%nodes are distributed between bed and surface accordingly to the given exponent
	821	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
	822	end
	823	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	824
[13692]	825	%Extrude elements
	826	elements3d=[];
	827	for i=1:numlayers-1,
	828	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
	829	end
	830	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	831
[13692]	832	%Keep a trace of lower and upper nodes
[17590]	833	lowervertex=NaN*ones(number_nodes3d,1);
	834	uppervertex=NaN*ones(number_nodes3d,1);
	835	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
	836	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
	837	md.mesh.lowervertex=lowervertex;
	838	md.mesh.uppervertex=uppervertex;
[13005]	839
[13692]	840	%same for lower and upper elements
[17590]	841	lowerelements=NaN*ones(number_el3d,1);
	842	upperelements=NaN*ones(number_el3d,1);
	843	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
	844	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
	845	md.mesh.lowerelements=lowerelements;
	846	md.mesh.upperelements=upperelements;
[13005]	847
[13692]	848	%Save old mesh
	849	md.mesh.x2d=md.mesh.x;
	850	md.mesh.y2d=md.mesh.y;
	851	md.mesh.elements2d=md.mesh.elements;
	852	md.mesh.numberofelements2d=md.mesh.numberofelements;
	853	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]	854
[13692]	855	%Build global 3d mesh
	856	md.mesh.elements=elements3d;
	857	md.mesh.x=x3d;
	858	md.mesh.y=y3d;
	859	md.mesh.z=z3d;
	860	md.mesh.numberofelements=number_el3d;
	861	md.mesh.numberofvertices=number_nodes3d;
	862	md.mesh.numberoflayers=numlayers;
[13005]	863
[13692]	864	%Ok, now deal with the other fields from the 2d mesh:
[13005]	865
[19048]	866	%bedinfo and surface info
	867	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
	868	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
	869	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
	870
[13692]	871	%lat long
	872	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
	873	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[22324]	874	md.mesh.scale_factor=project3d(md,'vector',md.mesh.scale_factor,'type','node');
[13005]	875
[19048]	876	md.geometry=extrude(md.geometry,md);
	877	md.friction = extrude(md.friction,md);
	878	md.inversion = extrude(md.inversion,md);
[19527]	879	md.smb = extrude(md.smb,md);
[19048]	880	md.initialization = extrude(md.initialization,md);
[13005]	881
[19050]	882	md.flowequation=md.flowequation.extrude(md);
[19048]	883	md.stressbalance=extrude(md.stressbalance,md);
[19050]	884	md.thermal=md.thermal.extrude(md);
	885	md.masstransport=md.masstransport.extrude(md);
[20460]	886	md.levelset=extrude(md.levelset,md);
[19048]	887	md.calving=extrude(md.calving,md);
[23652]	888	md.frontalforcings=extrude(md.frontalforcings,md);
[19048]	889	md.hydrology = extrude(md.hydrology,md);
[25118]	890	md.solidearth = extrude(md.solidearth,md);
[24469]	891	md.dsl = extrude(md.dsl,md);
[13005]	892
[13692]	893	%connectivity
[17991]	894	if ~isnan(md.mesh.elementconnectivity)
	895	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
	896	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
	897	for i=2:numlayers-1,
	898	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
	899	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
	900	end
	901	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13692]	902	end
[13005]	903
[19048]	904	md.materials=extrude(md.materials,md);
	905	md.damage=extrude(md.damage,md);
	906	md.mask=extrude(md.mask,md);
	907	md.qmu=extrude(md.qmu,md);
	908	md.basalforcings=extrude(md.basalforcings,md);
[21808]	909	md.outputdefinition=extrude(md.outputdefinition,md);
[13005]	910
[13692]	911	%increase connectivity if less than 25:
	912	if md.mesh.average_vertex_connectivity<=25,
	913	md.mesh.average_vertex_connectivity=100;
	914	end
[13005]	915	end % }}}
[13692]	916	function md = structtomodel(md,structmd) % {{{
[8952]	917
[13692]	918	if ~isstruct(structmd) error('input model is not a structure'); end
[8952]	919
[13692]	920	%loaded model is a struct, initialize output and recover all fields
	921	md = structtoobj(model,structmd);
[8952]	922
[13692]	923	%Old field now classes
	924	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
	925	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]	926
[13692]	927	%Field name change
	928	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	929	if isfield(structmd,'p'), md.friction.p=structmd.p; end
	930	if isfield(structmd,'q'), md.friction.q=structmd.p; end
[18378]	931	if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
[18068]	932	if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
[18378]	933	if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
[19527]	934	if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
[13692]	935	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
	936	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
	937	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
	938	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
[17610]	939	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
[13692]	940	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
	941	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
	942	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]	943	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]	944	if isfield(structmd,'g'), md.constants.g=structmd.g; end
	945	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
[19527]	946	if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
[18068]	947	if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
[13692]	948	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
	949	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	950	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
	951	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
	952	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
	953	if isfield(structmd,'riftproperties'), %old implementation
	954	md.rifts=rifts();
	955	md.rifts.riftproperties=structmd.riftproperties;
	956	md.rifts.riftstruct=structmd.rifts;
	957	md.rifts.riftproperties=structmd.riftinfo;
	958	end
	959	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
	960	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
	961	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
	962	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
	963	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
	964	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
	965	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
	966	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
	967	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
	968	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
	969	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
	970	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
	971	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
	972	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
	973	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
	974	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
	975	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
	976	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
	977	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
	978	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
	979	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
	980	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]	981	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
	982	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
	983	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
	984	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
	985	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]	986	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
	987	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
	988	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
	989	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]	990	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]	991	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
	992	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
	993	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]	994	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
	995	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]	996	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
	997	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
	998	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
	999	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]	1000	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]	1001	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]	1002	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
	1003	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
	1004	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
	1005	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
	1006	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
	1007	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
	1008	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
	1009	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
	1010	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
	1011	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
	1012	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
	1013	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
	1014	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
	1015	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
	1016	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
	1017	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
	1018	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
	1019	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
	1020	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
	1021	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
[17590]	1022	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
[13692]	1023	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
[17590]	1024	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
[13692]	1025	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
	1026	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
	1027	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
	1028	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
	1029	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
	1030	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
	1031	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
[22324]	1032	if isfield(structmd,'scale_factor'), md.mesh.scale_factor=structmd.scale_factor; end
[13692]	1033	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
	1034	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
	1035	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
	1036	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
	1037	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
	1038	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
	1039	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
	1040	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
	1041	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
	1042	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
	1043	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
	1044	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
	1045	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
	1046	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
	1047	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
	1048	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
[17610]	1049	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
[13692]	1050	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
	1051	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
	1052	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
	1053	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]	1054	if isfield(structmd,'edges'),
	1055	md.mesh.edges=structmd.edges;
	1056	md.mesh.edges(isnan(md.mesh.edges))=-1;
	1057	end
[13692]	1058	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
	1059	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
	1060	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
[15771]	1061	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]	1062	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
	1063	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]	1064
[13692]	1065	if isnumeric(md.verbose),
	1066	md.verbose=verbose;
	1067	end
[15768]	1068
[13692]	1069	if isfield(structmd,'spcvelocity'),
[15771]	1070	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1071	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1072	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1073	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
	1074	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
	1075	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]	1076	end
	1077	if isfield(structmd,'spcvx'),
[15771]	1078	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1079	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]	1080	end
	1081	if isfield(structmd,'spcvy'),
[15771]	1082	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1083	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]	1084	end
	1085	if isfield(structmd,'spcvz'),
[15771]	1086	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1087	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]	1088	end
[14620]	1089	if isfield(structmd,'pressureload'),
	1090	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]	1091	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
	1092	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
	1093	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]	1094	end
[13692]	1095	end
	1096	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
	1097	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
	1098	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
	1099	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
	1100	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
	1101	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
	1102	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
	1103	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
	1104	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
	1105	end
	1106	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
	1107	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
	1108	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
	1109	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
	1110	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
	1111	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
	1112	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
	1113	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
	1114	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
	1115	end
	1116	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
	1117	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
	1118	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
	1119	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
	1120	end
	1121	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
	1122	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
[17941]	1123	if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
[13692]	1124	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
	1125	end
	1126	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
	1127	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
	1128	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
	1129	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
	1130	end
	1131	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
	1132	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
	1133	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
	1134	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
	1135	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
	1136	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
	1137	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
	1138	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
	1139	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
	1140	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
	1141	end
[11659]	1142
[13692]	1143	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
	1144	md.thermal.stabilization=2;
[15767]	1145	md.masstransport.stabilization=1;
[13692]	1146	md.balancethickness.stabilization=1;
	1147	end
[15767]	1148	if isnumeric(md.masstransport.hydrostatic_adjustment)
	1149	if md.masstransport.hydrostatic_adjustment==269,
	1150	md.masstransport.hydrostatic_adjustment='Incremental';
[13692]	1151	else
[15767]	1152	md.masstransport.hydrostatic_adjustment='Absolute';
[13692]	1153	end
	1154	end
[8952]	1155
[13692]	1156	%New fields
[19124]	1157	if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1158	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
	1159	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
	1160	end
[19124]	1161	if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1162	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
	1163	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
	1164	end
	1165	if ~isfield(structmd,'diagnostic_ref');
[15771]	1166	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]	1167	end
[14529]	1168	if ~isfield(structmd,'loadingforce');
[15771]	1169	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]	1170	end
[15768]	1171
	1172	%2013 August 9
	1173	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
	1174	disp('Recovering old prognostic class');
	1175	md.masstransport=masstransport(structmd.prognostic);
	1176	end
[15771]	1177	%2013 August 9
[15775]	1178	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
[15771]	1179	disp('Recovering old diagnostic class');
[15775]	1180	md.stressbalance=stressbalance(structmd.diagnostic);
[15771]	1181	end
[19642]	1182	%2014 January 9th
[21148]	1183	if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
[19642]	1184	disp('Recovering old surfaceforcings class');
	1185	mass_balance=structmd.surfaceforcings.mass_balance;
	1186	md.smb=SMB();
	1187	md.smb.mass_balance=mass_balance;
	1188	end
	1189	%2015 September 10
[21148]	1190	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
[19642]	1191	disp('Recovering old SMB class');
	1192	md.smb=SMBforcing(structmd.surfaceforcings);
	1193	end
[21148]	1194	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
	1195	disp('Recovering old SMBhenning class');
	1196	md.smb=SMBhenning(structmd.surfaceforcings);
	1197	end
[13692]	1198	end% }}}
	1199	function md = setdefaultparameters(md) % {{{
[8926]	1200
[13692]	1201	%initialize subclasses
[17558]	1202	md.mesh = mesh2d();
[13692]	1203	md.mask = mask();
	1204	md.constants = constants();
	1205	md.geometry = geometry();
	1206	md.initialization = initialization();
[19527]	1207	md.smb = SMBforcing();
[13692]	1208	md.basalforcings = basalforcings();
	1209	md.friction = friction();
	1210	md.rifts = rifts();
[25118]	1211	md.solidearth = solidearth();
[24469]	1212	md.dsl = dsl();
[13692]	1213	md.timestepping = timestepping();
	1214	md.groundingline = groundingline();
	1215	md.materials = matice();
[16160]	1216	md.damage = damage();
[13692]	1217	md.flowequation = flowequation();
	1218	md.debug = debug();
[14558]	1219	md.verbose = verbose();
[22296]	1220	md.settings = issmsettings();
[17932]	1221	md.toolkits = toolkits();
[13692]	1222	md.cluster = generic();
	1223	md.balancethickness = balancethickness();
[17079]	1224	md.stressbalance = stressbalance();
[14555]	1225	md.hydrology = hydrologyshreve();
[17079]	1226	md.masstransport = masstransport();
[13692]	1227	md.thermal = thermal();
	1228	md.steadystate = steadystate();
	1229	md.transient = transient();
[22040]	1230	md.levelset = levelset();
[18757]	1231	md.calving = calving();
[23652]	1232	md.frontalforcings = frontalforcings();
[25066]	1233	md.gia = giamme();
[22955]	1234	md.esa = esa();
[22040]	1235	md.love = fourierlove();
[21260]	1236	md.esa = esa();
[13692]	1237	md.autodiff = autodiff();
	1238	md.inversion = inversion();
	1239	md.qmu = qmu();
[22955]	1240	md.amr = amr();
[13692]	1241	md.radaroverlay = radaroverlay();
	1242	md.results = struct();
[16388]	1243	md.outputdefinition = outputdefinition();
[13692]	1244	md.miscellaneous = miscellaneous();
	1245	md.private = private();
	1246	end
	1247	%}}}
[17483]	1248	function md = tetras(md,varargin) % {{{
	1249	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
	1250	%
	1251	% Usage:
	1252	% md=tetra(md)
	1253
	1254	if ~isa(md.mesh,'mesh3dprisms')
	1255	error('mesh is not a 3d prismatic mesh');
	1256	end
	1257
	1258	%Initialize tetra mesh
	1259	md.mesh=mesh3dtetras(md.mesh);
	1260
[17754]	1261	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
	1262	steiner = 0;
	1263	nbv = md.mesh.numberofvertices;
	1264	nbt = 3*md.mesh.numberofelements;
	1265	elements = zeros(nbt,4);
	1266	for i=1:md.mesh.numberofelements
	1267	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
	1268	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
	1269	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1270	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1271	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1272	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1273	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1274	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1275	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
	1276	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
	1277	elements(end+1,:) = [v2 v3 v5 v7];
	1278	elements(end+1,:) = [v3 v5 v6 v7];
	1279	elements(end+1,:) = [v1 v3 v6 v7];
	1280	elements(end+1,:) = [v1 v4 v6 v7];
	1281	elements(end+1,:) = [v4 v5 v6 v7];
	1282	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1283	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
	1284	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1285	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1286	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1287	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1288	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
	1289	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1290	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1291	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1292	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1293	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
[18142]	1294	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
[17754]	1295	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1296	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1297	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
	1298	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1299	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1300	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
	1301	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1302	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1303	elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
	1304	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1305	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1306	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1307	elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
	1308	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1309	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
	1310	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1311	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1312	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1313	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1314	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1315	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1316	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
	1317	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
	1318	elements(end+1,:) = [v2 v5 v6 v7];
	1319	elements(end+1,:) = [v2 v3 v6 v7];
	1320	elements(end+1,:) = [v3 v4 v6 v7];
	1321	elements(end+1,:) = [v1 v3 v4 v7];
	1322	elements(end+1,:) = [v4 v5 v6 v7];
	1323	else
	1324	error('Case not supported'); %not supposed to happen!
	1325	end
[17774]	1326	%Reorder elements to make sure they are direct
	1327	for j=1:3
	1328	element = elements(3*(i-1)+j,:);
	1329	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
	1330	if det(matrix)>0,
	1331	elements(3*(i-1)+j,1)=element(2);
	1332	elements(3*(i-1)+j,2)=element(1);
	1333	end
	1334	end
[17754]	1335	end
	1336	%%Split in 3 tetras
	1337	%subelement1 = [1 2 3 5];
	1338	%subelement2 = [4 6 5 1];
	1339	%subelement3 = [5 6 3 1];
	1340	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
[17774]	1341	if steiner==0,
	1342	disp('No Steiner point required to split prismatic mesh into tets');
	1343	else
	1344	disp([num2str(steiner) ' Steiner points had to be included'])
	1345	error('Steiner point not supported yet');
	1346	end
[17754]	1347
[17483]	1348	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
	1349
	1350	md.mesh.elements=elements;
	1351	md.mesh.numberofelements=size(elements,1);
	1352
	1353	%p and q (same deal, except for element that are on the bedrock: )
[17774]	1354	if ~isnan(md.friction.p),
	1355	md.friction.p=md.friction.p(pos_elements);
	1356	md.friction.q=md.friction.q(pos_elements);
	1357	end
[17483]	1358
	1359	%elementstype
	1360	if ~isnan(md.flowequation.element_equation)
	1361	oldelements_type=md.flowequation.element_equation;
	1362	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
	1363	end
	1364
	1365	%connectivity
	1366	md.mesh.elementconnectivity=NaN;
	1367
	1368	%materials
[17774]	1369	if ~isnan(md.materials.rheology_n),
	1370	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
	1371	end
[17483]	1372
	1373	%increase connectivity if less than 25:
	1374	if md.mesh.average_vertex_connectivity<=25,
	1375	md.mesh.average_vertex_connectivity=100;
	1376	end
	1377	end % }}}
[19040]	1378	function disp(self) % {{{
	1379	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
	1380	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
	1381	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
	1382	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
[19527]	1383	disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
[19040]	1384	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
	1385	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
	1386	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
	1387	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
	1388	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
	1389	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
	1390	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
	1391	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
[25118]	1392	disp(sprintf('%19s: %-22s -- %s','solidearth' ,['[1x1 ' class(self.solidearth) ']'],'solidearth inputs and settings'));
[24469]	1393	disp(sprintf('%19s: %-22s -- %s','dsl' ,['[1x1 ' class(self.dsl) ']'],'dynamic sea-level '));
[19040]	1394	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
	1395	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
	1396	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
	1397	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
	1398	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
	1399	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
	1400	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
	1401	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
	1402	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
	1403	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
	1404	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
	1405	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
	1406	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
[21544]	1407	disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
[19040]	1408	disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
[23652]	1409	disp(sprintf('%19s: %-22s -- %s','frontalforcings' ,['[1x1 ' class(self.frontalforcings) ']'],'parameters for frontalforcings'));
[22955]	1410	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
[21260]	1411	disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
[22955]	1412	disp(sprintf('%19s: %-22s -- %s','love' ,['[1x1 ' class(self.love) ']'],'parameters for love solution'));
[19040]	1413	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
	1414	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
	1415	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
[21674]	1416	disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
[19040]	1417	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
	1418	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
	1419	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
	1420	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
[13692]	1421	end % }}}
[19040]	1422	function memory(self) % {{{
[15106]	1423
[14611]	1424	disp(sprintf('\nMemory imprint:\n'));
[14307]	1425
[14603]	1426	fields=properties('model');
	1427	mem=0;
[15106]	1428
[14603]	1429	for i=1:length(fields),
[19040]	1430	field=self.(fields{i});
[14603]	1431	s=whos('field');
	1432	mem=mem+s.bytes/1e6;
[14611]	1433	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]	1434	end
[14603]	1435	disp(sprintf('%19s--%10s','--------------','--------------'));
	1436	disp(sprintf('%19s: %g Mb','Total',mem));
[14307]	1437	end % }}}
[19040]	1438	function netcdf(self,filename) % {{{
[14603]	1439	%NETCDF - save model as netcdf
	1440	%
	1441	% Usage:
	1442	% netcdf(md,filename)
	1443	%
	1444	% Example:
	1445	% netcdf(md,'model.nc');
	1446
	1447	disp('Saving model as NetCDF');
	1448	%1. Create NetCDF file
	1449	ncid=netcdf.create(filename,'CLOBBER');
	1450	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[19040]	1451	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
[14603]	1452	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
	1453	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
	1454
[14611]	1455	%Preallocate variable id, needed to write variables in netcdf file
[14631]	1456	var_id=zeros(1000,1);%preallocate
[14609]	1457
	1458	for step=1:2,
	1459	counter=0;
[19040]	1460	[var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
[14609]	1461	if step==1, netcdf.endDef(ncid); end
[14603]	1462	end
[14611]	1463
[14631]	1464	if counter>1000,
	1465	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]	1466	end
	1467
	1468	netcdf.close(ncid)
[14603]	1469	end % }}}
[19040]	1470	function xylim(self) % {{{
[14405]	1471
[19040]	1472	xlim([min(self.mesh.x) max(self.mesh.x)]);
	1473	ylim([min(self.mesh.y) max(self.mesh.y)])
[14405]	1474	end % }}}
[15316]	1475	function md=upload(md) % {{{
	1476	%the goal of this routine is to upload the model onto a server, and to empty it.
	1477	%So first, save the model with a unique name and upload the file to the server:
	1478	random_part=fix(rand(1)*10000);
	1479	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
	1480	eval(['save ' id ' md']);
	1481
	1482	%Now, upload the file:
	1483	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
	1484
	1485	%Now, empty this model of everything except settings, and record name of file we just uploaded!
	1486	settings_back=md.settings;
	1487	md=model();
	1488	md.settings=settings_back;
	1489	md.settings.upload_filename=id;
	1490
	1491	%get locally rid of file that was uploaded
	1492	eval(['delete ' id]);
	1493
	1494	end % }}}
	1495	function md=download(md) % {{{
[15643]	1496
[15316]	1497	%the goal of this routine is to download the internals of the current model from a server, because
	1498	%this model is empty, except for the settings which tell us where to go and find this model!
[15643]	1499
[15316]	1500	%Download the file:
	1501	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
	1502
	1503	name=md.settings.upload_filename;
	1504
	1505	%Now, load this model:
	1506	md=loadmodel(md.settings.upload_filename);
	1507
	1508	%get locally rid of file that was downloaded
	1509	eval(['delete ' name]);
	1510
	1511	end % }}}
[22955]	1512	function savemodeljs(md,modelname,websiteroot,varargin) % {{{
	1513
[19879]	1514	%the goal of this routine is to save the model as a javascript array that can be included in any html
	1515	%file:
	1516
[22955]	1517	options=pairoptions(varargin{:});
	1518	optimization=getfieldvalue(options,'optimize',0);
	1519
	1520
[19879]	1521	%disp:
[19894]	1522	disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
[19879]	1523
	1524	%open file for writing and declare the model:
[19894]	1525	fid=fopen([websiteroot '/js/' modelname '.js'],'w');
[19879]	1526	fprintf(fid,'var %s=new model();\n',modelname);
	1527
	1528	%now go through all the classes and fwrite all the corresponding fields:
	1529
	1530	fields=properties('model');
	1531	for i=1:length(fields),
	1532	field=fields{i};
	1533
	1534	%Some properties do not need to be saved
[19894]	1535	if ismember(field,{'results','cluster' }),
[19879]	1536	continue;
	1537	end
	1538
[22955]	1539	%some optimization:
	1540	if optimization==1,
	1541	%optimize for plotting only:
	1542	if ~ismember(field,{'geometry','mesh','mask'}),
	1543	continue;
	1544	end
	1545	end
	1546
[19879]	1547	%Check that current field is an object
	1548	if ~isobject(md.(field))
	1549	error(['field ''' char(field) ''' is not an object']);
	1550	end
	1551
	1552	%savemodeljs for current object
	1553	%disp(['javascript saving ' field '...']);
	1554	savemodeljs(md.(field),fid,modelname);
	1555	end
	1556
	1557	%done, close file:
	1558	fclose(fid);
	1559	end
[13692]	1560	end
[8926]	1561	end

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