Context Navigation

source: issm/trunk-jpl/src/m/classes/model.m@ 25168

Last change on this file since 25168 was 25168, checked in by jdquinn, 5 years ago
BUG: Corrected high-level bugs for test2010.py
File size: 72.2 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
[21260]	127	%2016 October 11
[21702]	128	if isa(md.esa,'double'); md.esa=esa(); end
[21545]	129	%2017 February 10th
[23434]	130	if isa(md.settings,'settings'), %this 'isa' verification: 2018 October 24th
	131	if md.settings.solver_residue_threshold==0,
	132	md.settings.solver_residue_threshold = 1e-6;
	133	end
[21545]	134	end
[21667]	135	%2017 April 10th
[25066]	136	if isa(md.gia,'gia'), md.gia=giamme(); end
[21702]	137	%2017 May 4th
	138	if isa(md.amr,'double'); md.amr=amr(); end
[22019]	139	%2017 Aug 29th
[22040]	140	if isa(md.love,'double'); md.love=fourierlove(); end
[22194]	141	%2017 Oct 26th
	142	if isa(md.calving,'calvingdev')
	143	disp('Warning: calvingdev is now calvingvonmises');
	144	md.calving=calvingvonmises(md.calving);
	145	end
[22955]	146	%2017 Dec 21st (needs to be here)
	147	if isempty(md.settings)
	148	disp('Warning: md.settings had to be reset, make sure to adjust md.settings.output_frequency and other fields');
	149	md.settings = issmsettings();
	150	end
[23503]	151	%2018 Dec 1st
	152	if md.settings.sb_coupling_frequency==0
	153	md.settings.sb_coupling_frequency=1;
	154	end
[23652]	155	%2019 Jan..
	156	if isa(md.frontalforcings,'double');
[24476]	157	if(isprop('meltingrate',md.calving) & ~isnan(md.calving.meltingrate))
[23652]	158	disp('Warning: md.calving.meltingrate is now in md.frontalforcings');
	159	end
	160	md.frontalforcings=frontalforcings(md.calving);
	161	end
[23758]	162	%2019 Feb 26
	163	if isa(md.settings.results_on_nodes,'double')
	164	if md.settings.results_on_nodes == 0
	165	md.settings.results_on_nodes = {};
	166	else
	167	md.settings.results_on_nodes = {'all'};
	168	end
	169	end
[23814]	170	%2019 Mar 28
[23984]	171	if isa(md.smb,'SMBcomponents') \| isa(md.smb,'SMBmeltcomponents') \| isa(md.smb,'SMBforcing') \| isa(md.smb,'SMBgemb')
	172	if isa(md.smb.isclimatology,'double')
	173	if prod(size(md.smb.isclimatology)) ~= 1
	174	md.smb.isclimatology = 0;
	175	end
[23814]	176	end
	177	end
[24474]	178	%2019 Dec 16
[24510]	179	if isa(md.dsl,'double') \| isempty(md.dsl.compute_fingerprints)
[24474]	180	md.dsl=dsl();
	181	end
[24738]	182	%2020 April 24
	183	if isa(md.smb,'SMBgemb')
	184	if isa(md.smb.isconstrainsurfaceT,'double')
	185	if prod(size(md.smb.isconstrainsurfaceT)) ~= 1
	186	md.smb.isconstrainsurfaceT = 0;
	187	end
	188	end
	189	end
[13692]	190	end% }}}
	191	end
	192	methods
	193	function md = model(varargin) % {{{
[8926]	194
[13692]	195	switch nargin
	196	case 0
	197	md=setdefaultparameters(md);
[18492]	198	case 1
[19087]	199	error('model constructor not supported yet');
[18503]	200
[13692]	201	otherwise
	202	error('model constructor error message: 0 of 1 argument only in input.');
	203	end
	204	end
	205	%}}}
	206	function md = checkmessage(md,string) % {{{
	207	if(nargout~=1) error('wrong usage, model must be an output'); end
	208	disp(['model not consistent: ' string]);
	209	md.private.isconsistent=false;
	210	end
	211	%}}}
	212	function md = collapse(md)% {{{
	213	%COLLAPSE - collapses a 3d mesh into a 2d mesh
	214	%
	215	% This routine collapses a 3d model into a 2d model
	216	% and collapses all the fileds of the 3d model by
	217	% taking their depth-averaged values
	218	%
	219	% Usage:
	220	% md=collapse(md)
	221	%
	222	% See also: EXTRUDE, MODELEXTRACT
[13005]	223
[13692]	224	%Check that the model is really a 3d model
[17687]	225	if ~strcmp(md.mesh.elementtype(),'Penta'),
[13692]	226	error('collapse error message: only 3d mesh can be collapsed')
	227	end
[13005]	228
[17724]	229	%Start with changing all the fields from the 3d mesh
[13005]	230
[21827]	231	%dealing with the friction law
[13692]	232	%drag is limited to nodes that are on the bedrock.
[18775]	233	if isa(md.friction,'friction'),
	234	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	235	md.friction.p=project2d(md,md.friction.p,1);
	236	md.friction.q=project2d(md,md.friction.q,1);
[21819]	237	elseif isa(md.friction,'frictioncoulomb'),
	238	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	239	md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1);
	240	md.friction.p=project2d(md,md.friction.p,1);
	241	md.friction.q=project2d(md,md.friction.q,1);
[18775]	242	elseif isa(md.friction,'frictionhydro'),
	243	md.friction.q=project2d(md,md.friction.q,1);
	244	md.friction.C=project2d(md,md.friction.C,1);
	245	md.friction.As=project2d(md,md.friction.As,1);
[18798]	246	md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
[18775]	247	elseif isa(md.friction,'frictionwaterlayer'),
	248	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	249	md.friction.p=project2d(md,md.friction.p,1);
	250	md.friction.q=project2d(md,md.friction.q,1);
	251	md.friction.water_layer=project2d(md,md.friction.water_layer,1);
	252	elseif isa(md.friction,'frictionweertman'),
	253	md.friction.C=project2d(md,md.friction.C,1);
	254	md.friction.m=project2d(md,md.friction.m,1);
[19720]	255	elseif isa(md.friction,'frictionweertmantemp'),
	256	md.friction.C=project2d(md,md.friction.C,1);
	257	md.friction.m=project2d(md,md.friction.m,1);
	258	else
	259	disp('friction type not supported');
[21827]	260	end
[13005]	261
[13692]	262	%observations
	263	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
	264	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
	265	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
[24465]	266	if ~isnan(md.inversion.thickness_obs), md.inversion.thickness_obs=project2d(md,md.inversion.thickness_obs,md.mesh.numberoflayers); end;
[13692]	267	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
	268	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
	269	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
[19527]	270	if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
	271	md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
	272	elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
	273	md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
[13692]	274	end;
[13005]	275
[13692]	276	%results
	277	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
	278	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
	279	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
	280	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
[18578]	281	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[18506]	282	if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
[18578]	283	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
	284	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
	285	if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
[21417]	286	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
	287	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
[21530]	288	%giaivins
[25074]	289	if isa(md.gia,'giaivins'),
	290	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
	291	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
	292	end
[15021]	293
[13692]	294	%elementstype
	295	if ~isnan(md.flowequation.element_equation)
	296	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
	297	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]	298	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
	299	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
	300	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]	301	end
[13005]	302
[13692]	303	%boundary conditions
[15771]	304	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
	305	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
	306	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
	307	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
	308	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[24536]	309	if numel(md.masstransport.spcthickness)>1 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers); end
[21544]	310	if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
[21417]	311	if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
[13692]	312	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]	313
[18506]	314	% Hydrologydc variables
	315	if isa(md.hydrology,'hydrologydc');
	316	md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
	317	md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
	318	md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
	319	md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
	320	if(md.hydrology.isefficientlayer==1)
	321	md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
[21808]	322	end
	323	end
[18506]	324
[13692]	325	%materials
	326	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
	327	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]	328
	329	%damage:
[17940]	330	if md.damage.isdamage,
	331	md.damage.D=DepthAverage(md,md.damage.D);
	332	end
[13005]	333
[13692]	334	%special for thermal modeling:
[18378]	335	if ~isnan(md.basalforcings.groundedice_melting_rate),
	336	md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
	337	end
[21417]	338	if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
[18378]	339	md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
	340	end
[13692]	341	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]	342
[21417]	343	if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
	344	md.calving.coeff=project2d(md,md.calving.coeff,1);
	345	end
[23652]	346	if isprop(md.frontalforcings,'meltingrate') & ~isnan(md.frontalforcings.meltingrate),
	347	md.frontalforcings.meltingrate=project2d(md,md.frontalforcings.meltingrate,1);
[21417]	348	end
	349
[13692]	350	%update of connectivity matrix
	351	md.mesh.average_vertex_connectivity=25;
[13005]	352
[13692]	353	%Collapse the mesh
	354	nodes2d=md.mesh.numberofvertices2d;
	355	elements2d=md.mesh.numberofelements2d;
[13005]	356
[13692]	357	%parameters
	358	md.geometry.surface=project2d(md,md.geometry.surface,1);
	359	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
[17590]	360	md.geometry.base=project2d(md,md.geometry.base,1);
[18480]	361	if ~isnan(md.geometry.bed),
	362	md.geometry.bed=project2d(md,md.geometry.bed,1);
	363	end
[17991]	364
[24861]	365	if ~isnan(md.mask.ocean_levelset),
	366	md.mask.ocean_levelset=project2d(md,md.mask.ocean_levelset,1);
[18378]	367	end
	368	if ~isnan(md.mask.ice_levelset),
	369	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
	370	end
[13005]	371
[22955]	372	%lat long
	373	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
	374	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
	375
[21808]	376	%outputdefinitions
	377	for i=1:length(md.outputdefinition.definitions)
	378	if isobject(md.outputdefinition.definitions{i})
	379	%get subfields
	380	solutionsubfields=fields(md.outputdefinition.definitions{i});
	381	for j=1:length(solutionsubfields),
	382	field=md.outputdefinition.definitions{i}.(solutionsubfields{j});
	383	if length(field)==md.mesh.numberofvertices \| length(field)==md.mesh.numberofelements,
	384	md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1);
	385	end
	386	end
	387	end
	388	end
	389
[13692]	390	%Initialize with the 2d mesh
[17724]	391	mesh=mesh2d();
	392	mesh.x=md.mesh.x2d;
	393	mesh.y=md.mesh.y2d;
	394	mesh.numberofvertices=md.mesh.numberofvertices2d;
	395	mesh.numberofelements=md.mesh.numberofelements2d;
	396	mesh.elements=md.mesh.elements2d;
[21499]	397	if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end
	398	if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end
	399	mesh.epsg=md.mesh.epsg;
[22324]	400	if numel(md.mesh.scale_factor)==md.mesh.numberofvertices, mesh.scale_factor=project2d(md,md.mesh.scale_factor,1); end
[17991]	401	if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
	402	if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
[17724]	403	md.mesh=mesh;
[18738]	404	md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
	405	md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
[19955]	406	md.mesh.segments=contourenvelope(md.mesh);
[13005]	407
[13692]	408	end % }}}
[22955]	409	function md2 = extract(md,area,varargin) % {{{
[13692]	410	%extract - extract a model according to an Argus contour or flag list
	411	%
	412	% This routine extracts a submodel from a bigger model with respect to a given contour
	413	% md must be followed by the corresponding exp file or flags list
	414	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
	415	% If user wants every element outside the domain to be
[15564]	416	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]	417	% an empty string '' will be considered as an empty domain
	418	% a string 'all' will be considered as the entire domain
	419	%
	420	% Usage:
	421	% md2=extract(md,area);
	422	%
	423	% Examples:
	424	% md2=extract(md,'Domain.exp');
	425	%
	426	% See also: EXTRUDE, COLLAPSE
[13005]	427
[13692]	428	%copy model
	429	md1=md;
[13005]	430
[22955]	431	%recover optoins:
	432	options=pairoptions(varargin{:});
	433
[13692]	434	%some checks
[22955]	435	if ((nargin<2) \| (nargout~=1)),
[13692]	436	help extract
	437	error('extract error message: bad usage');
	438	end
[13005]	439
[13692]	440	%get elements that are inside area
	441	flag_elem=FlagElements(md1,area);
	442	if ~any(flag_elem),
	443	error('extracted model is empty');
	444	end
[13005]	445
[13692]	446	%kick out all elements with 3 dirichlets
[22955]	447	if getfieldvalue(options,'spccheck',1)
	448	spc_elem=find(~flag_elem);
	449	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
	450	flag=ones(md1.mesh.numberofvertices,1);
	451	flag(spc_node)=0;
	452	pos=find(sum(flag(md1.mesh.elements),2)==0);
	453	flag_elem(pos)=0;
	454	end
[13005]	455
[13692]	456	%extracted elements and nodes lists
	457	pos_elem=find(flag_elem);
	458	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]	459
[13692]	460	%keep track of some fields
	461	numberofvertices1=md1.mesh.numberofvertices;
	462	numberofelements1=md1.mesh.numberofelements;
	463	numberofvertices2=length(pos_node);
	464	numberofelements2=length(pos_elem);
	465	flag_node=zeros(numberofvertices1,1);
	466	flag_node(pos_node)=1;
[13005]	467
[13692]	468	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
	469	Pelem=zeros(numberofelements1,1);
	470	Pelem(pos_elem)=[1:numberofelements2]';
	471	Pnode=zeros(numberofvertices1,1);
	472	Pnode(pos_node)=[1:numberofvertices2]';
[13005]	473
[13857]	474	%renumber the elements (some nodes won't exist anymore)
[13692]	475	elements_1=md1.mesh.elements;
	476	elements_2=elements_1(pos_elem,:);
	477	elements_2(:,1)=Pnode(elements_2(:,1));
	478	elements_2(:,2)=Pnode(elements_2(:,2));
	479	elements_2(:,3)=Pnode(elements_2(:,3));
[17558]	480	if isa(md1.mesh,'mesh3dprisms'),
[13692]	481	elements_2(:,4)=Pnode(elements_2(:,4));
	482	elements_2(:,5)=Pnode(elements_2(:,5));
	483	elements_2(:,6)=Pnode(elements_2(:,6));
	484	end
[13005]	485
[13857]	486	%OK, now create the new model!
[13005]	487
[13857]	488	%take every field from model
[13692]	489	md2=md1;
[13005]	490
[13692]	491	%automatically modify fields
[13005]	492
[13692]	493	%loop over model fields
	494	model_fields=fields(md1);
	495	for i=1:length(model_fields),
	496	%get field
	497	field=md1.(model_fields{i});
	498	fieldsize=size(field);
	499	if isobject(field), %recursive call
	500	object_fields=fields(md1.(model_fields{i}));
	501	for j=1:length(object_fields),
	502	%get field
	503	field=md1.(model_fields{i}).(object_fields{j});
	504	fieldsize=size(field);
	505	%size = number of nodes * n
	506	if fieldsize(1)==numberofvertices1
	507	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
	508	elseif (fieldsize(1)==numberofvertices1+1)
	509	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]	510	%size = number of elements * n
[13692]	511	elseif fieldsize(1)==numberofelements1
	512	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
[21428]	513	elseif (fieldsize(1)==numberofelements1+1)
	514	md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
[13692]	515	end
	516	end
	517	else
	518	%size = number of nodes * n
	519	if fieldsize(1)==numberofvertices1
	520	md2.(model_fields{i})=field(pos_node,:);
	521	elseif (fieldsize(1)==numberofvertices1+1)
	522	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]	523	%size = number of elements * n
[13692]	524	elseif fieldsize(1)==numberofelements1
	525	md2.(model_fields{i})=field(pos_elem,:);
[21428]	526	elseif (fieldsize(1)==numberofelements1+1)
	527	md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
[13692]	528	end
	529	end
	530	end
[13005]	531
[13692]	532	%modify some specific fields
[13005]	533
[13692]	534	%Mesh
	535	md2.mesh.numberofelements=numberofelements2;
	536	md2.mesh.numberofvertices=numberofvertices2;
	537	md2.mesh.elements=elements_2;
[13005]	538
[13692]	539	%mesh.uppervertex mesh.lowervertex
[17558]	540	if isa(md1.mesh,'mesh3dprisms'),
[13692]	541	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
	542	pos=find(~isnan(md2.mesh.uppervertex));
	543	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]	544
[13692]	545	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
	546	pos=find(~isnan(md2.mesh.lowervertex));
	547	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]	548
[13692]	549	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
	550	pos=find(~isnan(md2.mesh.upperelements));
	551	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]	552
[13692]	553	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
	554	pos=find(~isnan(md2.mesh.lowerelements));
	555	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
	556	end
[13005]	557
[13692]	558	%Initial 2d mesh
[17558]	559	if isa(md1.mesh,'mesh3dprisms'),
[13692]	560	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
	561	pos_elem_2d=find(flag_elem_2d);
	562	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
	563	pos_node_2d=find(flag_node_2d);
[13005]	564
[13692]	565	md2.mesh.numberofelements2d=length(pos_elem_2d);
	566	md2.mesh.numberofvertices2d=length(pos_node_2d);
	567	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
	568	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
	569	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
	570	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]	571
[13692]	572	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
	573	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
	574	end
[13005]	575
[13692]	576	%Edges
[17686]	577	if(dimension(md.mesh)==2),
[17563]	578	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
	579	%renumber first two columns
	580	pos=find(md2.mesh.edges(:,4)~=-1);
	581	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
	582	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
	583	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
	584	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
	585	%remove edges when the 2 vertices are not in the domain.
	586	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
	587	%Replace all zeros by -1 in the last two columns
	588	pos=find(md2.mesh.edges(:,3)==0);
	589	md2.mesh.edges(pos,3)=-1;
	590	pos=find(md2.mesh.edges(:,4)==0);
	591	md2.mesh.edges(pos,4)=-1;
	592	%Invert -1 on the third column with last column (Also invert first two columns!!)
	593	pos=find(md2.mesh.edges(:,3)==-1);
	594	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
	595	md2.mesh.edges(pos,4)=-1;
	596	values=md2.mesh.edges(pos,2);
	597	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
	598	md2.mesh.edges(pos,1)=values;
	599	%Finally remove edges that do not belong to any element
	600	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
	601	md2.mesh.edges(pos,:)=[];
	602	end
[13692]	603	end
[13005]	604
[13692]	605	%Penalties
[15771]	606	if ~isnan(md2.stressbalance.vertex_pairing),
	607	for i=1:size(md1.stressbalance.vertex_pairing,1);
	608	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]	609	end
[15771]	610	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]	611	end
[15767]	612	if ~isnan(md2.masstransport.vertex_pairing),
	613	for i=1:size(md1.masstransport.vertex_pairing,1);
	614	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]	615	end
[15767]	616	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]	617	end
[13005]	618
[13692]	619	%recreate segments
[20322]	620	if isa(md1.mesh,'mesh2d') \| isa(md1.mesh','mesh3dsurface'),
[13692]	621	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	622	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
[19957]	623	md2.mesh.segments=contourenvelope(md2.mesh);
[13692]	624	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
	625	else
	626	%First do the connectivity for the contourenvelope in 2d
	627	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
	628	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
[19957]	629	segments=contourenvelope(md2.mesh);
[17565]	630	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
[13692]	631	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
	632	%Then do it for 3d as usual
	633	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	634	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	635	end
[13005]	636
[13692]	637	%Boundary conditions: Dirichlets on new boundary
	638	%Catch the elements that have not been extracted
	639	orphans_elem=find(~flag_elem);
	640	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
	641	%Figure out which node are on the boundary between md2 and md1
	642	nodestoflag1=intersect(orphans_node,pos_node);
	643	nodestoflag2=Pnode(nodestoflag1);
[23771]	644	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>1 & numel(md1.stressbalance.spcvz)>1,
[13692]	645	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]	646	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
	647	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]	648	else
[15771]	649	md2.stressbalance.spcvx(nodestoflag2)=NaN;
	650	md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]	651	disp(' ')
	652	disp('!! extract warning: spc values should be checked !!')
	653	disp(' ')
	654	end
	655	%put 0 for vz
[15771]	656	md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]	657	end
	658	if ~isnan(md1.thermal.spctemperature),
	659	md2.thermal.spctemperature(nodestoflag2,1)=1;
	660	end
[13005]	661
[13692]	662	%Results fields
	663	if isstruct(md1.results),
	664	md2.results=struct();
	665	solutionfields=fields(md1.results);
	666	for i=1:length(solutionfields),
[14230]	667	if isstruct(md1.results.(solutionfields{i}))
	668	%get subfields
[24134]	669	% loop over time steps
	670	for p=1:length(md1.results.(solutionfields{i}))
	671	current = md1.results.(solutionfields{i})(p);
	672	solutionsubfields=fields(current);
	673	for j=1:length(solutionsubfields),
	674	field=md1.results.(solutionfields{i})(p).(solutionsubfields{j});
[14230]	675	if length(field)==numberofvertices1,
[24134]	676	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_node);
[14230]	677	elseif length(field)==numberofelements1,
[24134]	678	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_elem);
[14230]	679	else
[24134]	680	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field;
[14230]	681	end
[24134]	682	end
[14230]	683	end
	684	else
	685	field=md1.results.(solutionfields{i});
[13692]	686	if length(field)==numberofvertices1,
[14230]	687	md2.results.(solutionfields{i})=field(pos_node);
[13692]	688	elseif length(field)==numberofelements1,
[14230]	689	md2.results.(solutionfields{i})=field(pos_elem);
[13692]	690	else
[14230]	691	md2.results.(solutionfields{i})=field;
[13692]	692	end
	693	end
	694	end
	695	end
[13005]	696
[21808]	697	%OutputDefinitions fields
	698	for i=1:length(md1.outputdefinition.definitions),
	699	if isobject(md1.outputdefinition.definitions{i})
	700	%get subfields
	701	solutionsubfields=fields(md1.outputdefinition.definitions{i});
	702	for j=1:length(solutionsubfields),
	703	field=md1.outputdefinition.definitions{i}.(solutionsubfields{j});
	704	if length(field)==numberofvertices1,
	705	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node);
	706	elseif length(field)==numberofelements1,
	707	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem);
	708	end
	709	end
	710	end
	711	end
	712
[13692]	713	%Keep track of pos_node and pos_elem
	714	md2.mesh.extractedvertices=pos_node;
	715	md2.mesh.extractedelements=pos_elem;
	716	end % }}}
	717	function md = extrude(md,varargin) % {{{
	718	%EXTRUDE - vertically extrude a 2d mesh
	719	%
	720	% vertically extrude a 2d mesh and create corresponding 3d mesh.
	721	% The vertical distribution can:
	722	% - follow a polynomial law
	723	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
	724	% - be discribed by a list of coefficients (between 0 and 1)
	725	%
	726	%
	727	% Usage:
	728	% md=extrude(md,numlayers,extrusionexponent);
	729	% md=extrude(md,numlayers,lowerexponent,upperexponent);
	730	% md=extrude(md,listofcoefficients);
	731	%
	732	% Example:
[18216]	733	% md=extrude(md,15,1.3);
	734	% md=extrude(md,15,1.3,1.2);
[13692]	735	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
	736	%
	737	% See also: MODELEXTRACT, COLLAPSE
[13005]	738
[13692]	739	%some checks on list of arguments
	740	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
	741	help extrude;
	742	error('extrude error message');
	743	end
[24511]	744	if numel(md.geometry.base)~=md.mesh.numberofvertices \|\| numel(md.geometry.surface)~=md.mesh.numberofvertices
	745	error('model has not been parameterized yet: base and/or surface not set');
	746	end
[13005]	747
[13692]	748	%Extrude the mesh
	749	if nargin==2, %list of coefficients
	750	clist=varargin{1};
	751	if any(clist<0) \| any(clist>1),
	752	error('extrusioncoefficients must be between 0 and 1');
	753	end
	754	extrusionlist=sort(unique([clist(:);0;1]));
	755	numlayers=length(extrusionlist);
	756	elseif nargin==3, %one polynomial law
	757	if varargin{2}<=0,
	758	help extrude;
	759	error('extrusionexponent must be >=0');
	760	end
	761	numlayers=varargin{1};
	762	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
	763	elseif nargin==4, %two polynomial laws
	764	numlayers=varargin{1};
	765	lowerexp=varargin{2};
	766	upperexp=varargin{3};
[13005]	767
[13692]	768	if varargin{2}<=0 \| varargin{3}<=0,
	769	help extrude;
	770	error('lower and upper extrusionexponents must be >=0');
	771	end
[13005]	772
[13692]	773	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
	774	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
	775	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]	776
[13692]	777	end
[13005]	778
[13692]	779	if numlayers<2,
	780	error('number of layers should be at least 2');
	781	end
[17686]	782	if strcmp(md.mesh.domaintype(),'3D')
[13692]	783	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
	784	end
[13005]	785
[13692]	786	%Initialize with the 2d mesh
[17558]	787	mesh2d = md.mesh;
	788	md.mesh=mesh3dprisms();
	789	md.mesh.x = mesh2d.x;
	790	md.mesh.y = mesh2d.y;
	791	md.mesh.elements = mesh2d.elements;
	792	md.mesh.numberofelements = mesh2d.numberofelements;
	793	md.mesh.numberofvertices = mesh2d.numberofvertices;
	794
	795	md.mesh.lat = mesh2d.lat;
	796	md.mesh.long = mesh2d.long;
[18558]	797	md.mesh.epsg = mesh2d.epsg;
[22324]	798	md.mesh.scale_factor = mesh2d.scale_factor;
[17558]	799
	800	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
	801	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
	802	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
	803	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
	804
	805	md.mesh.extractedvertices = mesh2d.extractedvertices;
	806	md.mesh.extractedelements = mesh2d.extractedelements;
	807
[13692]	808	x3d=[];
	809	y3d=[];
	810	z3d=[]; %the lower node is on the bed
	811	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
[17590]	812	bed3d=md.geometry.base;
[13005]	813
[13692]	814	%Create the new layers
	815	for i=1:numlayers,
	816	x3d=[x3d; md.mesh.x];
	817	y3d=[y3d; md.mesh.y];
	818	%nodes are distributed between bed and surface accordingly to the given exponent
	819	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
	820	end
	821	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	822
[13692]	823	%Extrude elements
	824	elements3d=[];
	825	for i=1:numlayers-1,
	826	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
	827	end
	828	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	829
[13692]	830	%Keep a trace of lower and upper nodes
[17590]	831	lowervertex=NaN*ones(number_nodes3d,1);
	832	uppervertex=NaN*ones(number_nodes3d,1);
	833	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
	834	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
	835	md.mesh.lowervertex=lowervertex;
	836	md.mesh.uppervertex=uppervertex;
[13005]	837
[13692]	838	%same for lower and upper elements
[17590]	839	lowerelements=NaN*ones(number_el3d,1);
	840	upperelements=NaN*ones(number_el3d,1);
	841	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
	842	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
	843	md.mesh.lowerelements=lowerelements;
	844	md.mesh.upperelements=upperelements;
[13005]	845
[13692]	846	%Save old mesh
	847	md.mesh.x2d=md.mesh.x;
	848	md.mesh.y2d=md.mesh.y;
	849	md.mesh.elements2d=md.mesh.elements;
	850	md.mesh.numberofelements2d=md.mesh.numberofelements;
	851	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]	852
[13692]	853	%Build global 3d mesh
	854	md.mesh.elements=elements3d;
	855	md.mesh.x=x3d;
	856	md.mesh.y=y3d;
	857	md.mesh.z=z3d;
	858	md.mesh.numberofelements=number_el3d;
	859	md.mesh.numberofvertices=number_nodes3d;
	860	md.mesh.numberoflayers=numlayers;
[13005]	861
[13692]	862	%Ok, now deal with the other fields from the 2d mesh:
[13005]	863
[19048]	864	%bedinfo and surface info
	865	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
	866	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
	867	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
	868
[13692]	869	%lat long
	870	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
	871	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[22324]	872	md.mesh.scale_factor=project3d(md,'vector',md.mesh.scale_factor,'type','node');
[13005]	873
[19048]	874	md.geometry=extrude(md.geometry,md);
	875	md.friction = extrude(md.friction,md);
	876	md.inversion = extrude(md.inversion,md);
[19527]	877	md.smb = extrude(md.smb,md);
[19048]	878	md.initialization = extrude(md.initialization,md);
[13005]	879
[19050]	880	md.flowequation=md.flowequation.extrude(md);
[19048]	881	md.stressbalance=extrude(md.stressbalance,md);
[19050]	882	md.thermal=md.thermal.extrude(md);
	883	md.masstransport=md.masstransport.extrude(md);
[20460]	884	md.levelset=extrude(md.levelset,md);
[19048]	885	md.calving=extrude(md.calving,md);
[23652]	886	md.frontalforcings=extrude(md.frontalforcings,md);
[19048]	887	md.hydrology = extrude(md.hydrology,md);
[25118]	888	md.solidearth = extrude(md.solidearth,md);
[24469]	889	md.dsl = extrude(md.dsl,md);
[13005]	890
[13692]	891	%connectivity
[17991]	892	if ~isnan(md.mesh.elementconnectivity)
	893	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
	894	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
	895	for i=2:numlayers-1,
	896	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
	897	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
	898	end
	899	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13692]	900	end
[13005]	901
[19048]	902	md.materials=extrude(md.materials,md);
	903	md.damage=extrude(md.damage,md);
	904	md.mask=extrude(md.mask,md);
	905	md.qmu=extrude(md.qmu,md);
	906	md.basalforcings=extrude(md.basalforcings,md);
[21808]	907	md.outputdefinition=extrude(md.outputdefinition,md);
[13005]	908
[13692]	909	%increase connectivity if less than 25:
	910	if md.mesh.average_vertex_connectivity<=25,
	911	md.mesh.average_vertex_connectivity=100;
	912	end
[13005]	913	end % }}}
[13692]	914	function md = structtomodel(md,structmd) % {{{
[8952]	915
[13692]	916	if ~isstruct(structmd) error('input model is not a structure'); end
[8952]	917
[13692]	918	%loaded model is a struct, initialize output and recover all fields
	919	md = structtoobj(model,structmd);
[8952]	920
[13692]	921	%Old field now classes
	922	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
	923	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]	924
[13692]	925	%Field name change
	926	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	927	if isfield(structmd,'p'), md.friction.p=structmd.p; end
	928	if isfield(structmd,'q'), md.friction.q=structmd.p; end
[18378]	929	if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
[18068]	930	if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
[18378]	931	if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
[19527]	932	if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
[13692]	933	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
	934	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
	935	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
	936	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
[17610]	937	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
[13692]	938	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
	939	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
	940	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]	941	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]	942	if isfield(structmd,'g'), md.constants.g=structmd.g; end
	943	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
[19527]	944	if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
[18068]	945	if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
[13692]	946	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
	947	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	948	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
	949	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
	950	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
	951	if isfield(structmd,'riftproperties'), %old implementation
	952	md.rifts=rifts();
	953	md.rifts.riftproperties=structmd.riftproperties;
	954	md.rifts.riftstruct=structmd.rifts;
	955	md.rifts.riftproperties=structmd.riftinfo;
	956	end
	957	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
	958	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
	959	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
	960	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
	961	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
	962	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
	963	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
	964	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
	965	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
	966	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
	967	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
	968	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
	969	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
	970	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
	971	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
	972	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
	973	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
	974	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
	975	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
	976	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
	977	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
	978	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]	979	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
	980	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
	981	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
	982	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
	983	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]	984	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
	985	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
	986	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
	987	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]	988	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]	989	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
	990	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
	991	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]	992	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
	993	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]	994	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
	995	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
	996	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
	997	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]	998	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]	999	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]	1000	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
	1001	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
	1002	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
	1003	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
	1004	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
	1005	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
	1006	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
	1007	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
	1008	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
	1009	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
	1010	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
	1011	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
	1012	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
	1013	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
	1014	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
	1015	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
	1016	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
	1017	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
	1018	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
	1019	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
[17590]	1020	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
[13692]	1021	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
[17590]	1022	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
[13692]	1023	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
	1024	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
	1025	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
	1026	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
	1027	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
	1028	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
	1029	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
[22324]	1030	if isfield(structmd,'scale_factor'), md.mesh.scale_factor=structmd.scale_factor; end
[13692]	1031	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
	1032	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
	1033	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
	1034	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
	1035	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
	1036	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
	1037	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
	1038	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
	1039	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
	1040	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
	1041	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
	1042	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
	1043	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
	1044	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
	1045	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
	1046	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
[17610]	1047	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
[13692]	1048	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
	1049	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
	1050	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
	1051	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]	1052	if isfield(structmd,'edges'),
	1053	md.mesh.edges=structmd.edges;
	1054	md.mesh.edges(isnan(md.mesh.edges))=-1;
	1055	end
[13692]	1056	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
	1057	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
	1058	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
[15771]	1059	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]	1060	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
	1061	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]	1062
[13692]	1063	if isnumeric(md.verbose),
	1064	md.verbose=verbose;
	1065	end
[15768]	1066
[13692]	1067	if isfield(structmd,'spcvelocity'),
[15771]	1068	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1069	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1070	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1071	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
	1072	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
	1073	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]	1074	end
	1075	if isfield(structmd,'spcvx'),
[15771]	1076	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1077	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]	1078	end
	1079	if isfield(structmd,'spcvy'),
[15771]	1080	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1081	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]	1082	end
	1083	if isfield(structmd,'spcvz'),
[15771]	1084	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1085	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]	1086	end
[14620]	1087	if isfield(structmd,'pressureload'),
	1088	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]	1089	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
	1090	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
	1091	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]	1092	end
[13692]	1093	end
	1094	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
	1095	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
	1096	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
	1097	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
	1098	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
	1099	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
	1100	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
	1101	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
	1102	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
	1103	end
	1104	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
	1105	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
	1106	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
	1107	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
	1108	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
	1109	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
	1110	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
	1111	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
	1112	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
	1113	end
	1114	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
	1115	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
	1116	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
	1117	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
	1118	end
	1119	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
	1120	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
[17941]	1121	if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
[13692]	1122	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
	1123	end
	1124	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
	1125	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
	1126	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
	1127	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
	1128	end
	1129	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
	1130	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
	1131	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
	1132	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
	1133	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
	1134	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
	1135	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
	1136	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
	1137	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
	1138	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
	1139	end
[11659]	1140
[13692]	1141	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
	1142	md.thermal.stabilization=2;
[15767]	1143	md.masstransport.stabilization=1;
[13692]	1144	md.balancethickness.stabilization=1;
	1145	end
[15767]	1146	if isnumeric(md.masstransport.hydrostatic_adjustment)
	1147	if md.masstransport.hydrostatic_adjustment==269,
	1148	md.masstransport.hydrostatic_adjustment='Incremental';
[13692]	1149	else
[15767]	1150	md.masstransport.hydrostatic_adjustment='Absolute';
[13692]	1151	end
	1152	end
[8952]	1153
[13692]	1154	%New fields
[19124]	1155	if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1156	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
	1157	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
	1158	end
[19124]	1159	if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1160	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
	1161	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
	1162	end
	1163	if ~isfield(structmd,'diagnostic_ref');
[15771]	1164	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]	1165	end
[14529]	1166	if ~isfield(structmd,'loadingforce');
[15771]	1167	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]	1168	end
[15768]	1169
	1170	%2013 August 9
	1171	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
	1172	disp('Recovering old prognostic class');
	1173	md.masstransport=masstransport(structmd.prognostic);
	1174	end
[15771]	1175	%2013 August 9
[15775]	1176	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
[15771]	1177	disp('Recovering old diagnostic class');
[15775]	1178	md.stressbalance=stressbalance(structmd.diagnostic);
[15771]	1179	end
[19642]	1180	%2014 January 9th
[21148]	1181	if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
[19642]	1182	disp('Recovering old surfaceforcings class');
	1183	mass_balance=structmd.surfaceforcings.mass_balance;
	1184	md.smb=SMB();
	1185	md.smb.mass_balance=mass_balance;
	1186	end
	1187	%2015 September 10
[21148]	1188	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
[19642]	1189	disp('Recovering old SMB class');
	1190	md.smb=SMBforcing(structmd.surfaceforcings);
	1191	end
[21148]	1192	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
	1193	disp('Recovering old SMBhenning class');
	1194	md.smb=SMBhenning(structmd.surfaceforcings);
	1195	end
[25119]	1196	if isfield(structmd,'slr'),
	1197	disp('Recovering old slr class');
	1198	md.solidearth.sealevel=structmd.slr.sealevel;
	1199	md.solidearth.planetradius=structmd.slr.planetradius;
	1200	md.solidearth.requested_outputs=structmd.slr.requested_outputs;
	1201	md.solidearth.transitions=structmd.slr.transitions;
	1202
	1203	md.solidearth.transitions=structmd.slr.transitions;
	1204	md.solidearth.settings.reltol=structmd.slr.reltol;
	1205	md.solidearth.settings.abstol=structmd.slr.abstol;
	1206	md.solidearth.settings.maxiter=structmd.slr.maxiter;
	1207	md.solidearth.settings.rigid=structmd.slr.rigid;
	1208	md.solidearth.settings.elastic=structmd.slr.elastic;
	1209	md.solidearth.settings.rotation=structmd.slr.rotation;
	1210	md.solidearth.settings.runfrequency=structmd.slr.geodetic_run_frequency;
	1211	md.solidearth.settings.computesealevelchange=structmd.slr.geodetic;
	1212	md.solidearth.settings.degacc=structmd.slr.degacc;
	1213	md.solidearth.settings.horiz=structmd.slr.horiz;
	1214	md.solidearth.settings.ocean_area_scaling=structmd.slr.ocean_area_scaling;
	1215
	1216	md.solidearth.surfaceload.icethicknesschange=structmd.slr.deltathickness;
	1217	md.solidearth.surfaceload.waterheightchange=structmd.slr.hydro_rate;
	1218
[25162]	1219	md.solidearth.lovenumbers.h=structmd.slr.love_h;
	1220	md.solidearth.lovenumbers.k=structmd.slr.love_k;
	1221	md.solidearth.lovenumbers.l=structmd.slr.love_l;
	1222	md.solidearth.lovenumbers.th=structmd.slr.tide_love_h;
	1223	md.solidearth.lovenumbers.tk=structmd.slr.tide_love_k;
	1224	md.solidearth.lovenumbers.tk2secular=structmd.slr.fluid_love;
[25119]	1225
	1226	md.solidearth.rotational.equatorialmoi=structmd.slr.equatorial_moi;
	1227	md.solidearth.rotational.polarmoi=structmd.slr.polar_moi;
	1228	md.solidearth.rotational.angularvelocity=structmd.slr.angular_velocity;
	1229	end
[13692]	1230	end% }}}
	1231	function md = setdefaultparameters(md) % {{{
[8926]	1232
[13692]	1233	%initialize subclasses
[17558]	1234	md.mesh = mesh2d();
[13692]	1235	md.mask = mask();
	1236	md.constants = constants();
	1237	md.geometry = geometry();
	1238	md.initialization = initialization();
[19527]	1239	md.smb = SMBforcing();
[13692]	1240	md.basalforcings = basalforcings();
	1241	md.friction = friction();
	1242	md.rifts = rifts();
[25118]	1243	md.solidearth = solidearth();
[24469]	1244	md.dsl = dsl();
[13692]	1245	md.timestepping = timestepping();
	1246	md.groundingline = groundingline();
	1247	md.materials = matice();
[16160]	1248	md.damage = damage();
[13692]	1249	md.flowequation = flowequation();
	1250	md.debug = debug();
[14558]	1251	md.verbose = verbose();
[22296]	1252	md.settings = issmsettings();
[17932]	1253	md.toolkits = toolkits();
[13692]	1254	md.cluster = generic();
	1255	md.balancethickness = balancethickness();
[17079]	1256	md.stressbalance = stressbalance();
[14555]	1257	md.hydrology = hydrologyshreve();
[17079]	1258	md.masstransport = masstransport();
[13692]	1259	md.thermal = thermal();
	1260	md.steadystate = steadystate();
	1261	md.transient = transient();
[22040]	1262	md.levelset = levelset();
[18757]	1263	md.calving = calving();
[23652]	1264	md.frontalforcings = frontalforcings();
[25168]	1265	md.gia = giamme();
[22955]	1266	md.esa = esa();
[22040]	1267	md.love = fourierlove();
[21260]	1268	md.esa = esa();
[13692]	1269	md.autodiff = autodiff();
	1270	md.inversion = inversion();
	1271	md.qmu = qmu();
[25168]	1272	md.amr = amr();
[13692]	1273	md.radaroverlay = radaroverlay();
	1274	md.results = struct();
[16388]	1275	md.outputdefinition = outputdefinition();
[13692]	1276	md.miscellaneous = miscellaneous();
	1277	md.private = private();
	1278	end
	1279	%}}}
[17483]	1280	function md = tetras(md,varargin) % {{{
	1281	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
	1282	%
	1283	% Usage:
	1284	% md=tetra(md)
	1285
	1286	if ~isa(md.mesh,'mesh3dprisms')
	1287	error('mesh is not a 3d prismatic mesh');
	1288	end
	1289
	1290	%Initialize tetra mesh
	1291	md.mesh=mesh3dtetras(md.mesh);
	1292
[17754]	1293	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
	1294	steiner = 0;
	1295	nbv = md.mesh.numberofvertices;
	1296	nbt = 3*md.mesh.numberofelements;
	1297	elements = zeros(nbt,4);
	1298	for i=1:md.mesh.numberofelements
	1299	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
	1300	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
	1301	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1302	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1303	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1304	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1305	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1306	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1307	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
	1308	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
	1309	elements(end+1,:) = [v2 v3 v5 v7];
	1310	elements(end+1,:) = [v3 v5 v6 v7];
	1311	elements(end+1,:) = [v1 v3 v6 v7];
	1312	elements(end+1,:) = [v1 v4 v6 v7];
	1313	elements(end+1,:) = [v4 v5 v6 v7];
	1314	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1315	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
	1316	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1317	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1318	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1319	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1320	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
	1321	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1322	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1323	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1324	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1325	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
[18142]	1326	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
[17754]	1327	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1328	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1329	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
	1330	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1331	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1332	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
	1333	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1334	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1335	elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
	1336	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1337	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1338	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1339	elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
	1340	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1341	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
	1342	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1343	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1344	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1345	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1346	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1347	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1348	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
	1349	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
	1350	elements(end+1,:) = [v2 v5 v6 v7];
	1351	elements(end+1,:) = [v2 v3 v6 v7];
	1352	elements(end+1,:) = [v3 v4 v6 v7];
	1353	elements(end+1,:) = [v1 v3 v4 v7];
	1354	elements(end+1,:) = [v4 v5 v6 v7];
	1355	else
	1356	error('Case not supported'); %not supposed to happen!
	1357	end
[17774]	1358	%Reorder elements to make sure they are direct
	1359	for j=1:3
	1360	element = elements(3*(i-1)+j,:);
	1361	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
	1362	if det(matrix)>0,
	1363	elements(3*(i-1)+j,1)=element(2);
	1364	elements(3*(i-1)+j,2)=element(1);
	1365	end
	1366	end
[17754]	1367	end
	1368	%%Split in 3 tetras
	1369	%subelement1 = [1 2 3 5];
	1370	%subelement2 = [4 6 5 1];
	1371	%subelement3 = [5 6 3 1];
	1372	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
[17774]	1373	if steiner==0,
	1374	disp('No Steiner point required to split prismatic mesh into tets');
	1375	else
	1376	disp([num2str(steiner) ' Steiner points had to be included'])
	1377	error('Steiner point not supported yet');
	1378	end
[17754]	1379
[17483]	1380	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
	1381
	1382	md.mesh.elements=elements;
	1383	md.mesh.numberofelements=size(elements,1);
	1384
	1385	%p and q (same deal, except for element that are on the bedrock: )
[17774]	1386	if ~isnan(md.friction.p),
	1387	md.friction.p=md.friction.p(pos_elements);
	1388	md.friction.q=md.friction.q(pos_elements);
	1389	end
[17483]	1390
	1391	%elementstype
	1392	if ~isnan(md.flowequation.element_equation)
	1393	oldelements_type=md.flowequation.element_equation;
	1394	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
	1395	end
	1396
	1397	%connectivity
	1398	md.mesh.elementconnectivity=NaN;
	1399
	1400	%materials
[17774]	1401	if ~isnan(md.materials.rheology_n),
	1402	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
	1403	end
[17483]	1404
	1405	%increase connectivity if less than 25:
	1406	if md.mesh.average_vertex_connectivity<=25,
	1407	md.mesh.average_vertex_connectivity=100;
	1408	end
	1409	end % }}}
[19040]	1410	function disp(self) % {{{
	1411	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
	1412	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
	1413	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
	1414	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
[19527]	1415	disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
[19040]	1416	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
	1417	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
	1418	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
	1419	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
	1420	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
	1421	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
	1422	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
	1423	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
[25118]	1424	disp(sprintf('%19s: %-22s -- %s','solidearth' ,['[1x1 ' class(self.solidearth) ']'],'solidearth inputs and settings'));
[24469]	1425	disp(sprintf('%19s: %-22s -- %s','dsl' ,['[1x1 ' class(self.dsl) ']'],'dynamic sea-level '));
[19040]	1426	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
	1427	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
	1428	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
	1429	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
	1430	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
	1431	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
	1432	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
	1433	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
	1434	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
	1435	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
	1436	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
	1437	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
	1438	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
[21544]	1439	disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
[19040]	1440	disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
[23652]	1441	disp(sprintf('%19s: %-22s -- %s','frontalforcings' ,['[1x1 ' class(self.frontalforcings) ']'],'parameters for frontalforcings'));
[22955]	1442	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
[21260]	1443	disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
[22955]	1444	disp(sprintf('%19s: %-22s -- %s','love' ,['[1x1 ' class(self.love) ']'],'parameters for love solution'));
[19040]	1445	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
	1446	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
	1447	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
[21674]	1448	disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
[19040]	1449	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
	1450	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
	1451	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
	1452	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
[13692]	1453	end % }}}
[19040]	1454	function memory(self) % {{{
[15106]	1455
[14611]	1456	disp(sprintf('\nMemory imprint:\n'));
[14307]	1457
[14603]	1458	fields=properties('model');
	1459	mem=0;
[15106]	1460
[14603]	1461	for i=1:length(fields),
[19040]	1462	field=self.(fields{i});
[14603]	1463	s=whos('field');
	1464	mem=mem+s.bytes/1e6;
[14611]	1465	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]	1466	end
[14603]	1467	disp(sprintf('%19s--%10s','--------------','--------------'));
	1468	disp(sprintf('%19s: %g Mb','Total',mem));
[14307]	1469	end % }}}
[19040]	1470	function netcdf(self,filename) % {{{
[14603]	1471	%NETCDF - save model as netcdf
	1472	%
	1473	% Usage:
	1474	% netcdf(md,filename)
	1475	%
	1476	% Example:
	1477	% netcdf(md,'model.nc');
	1478
	1479	disp('Saving model as NetCDF');
	1480	%1. Create NetCDF file
	1481	ncid=netcdf.create(filename,'CLOBBER');
	1482	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[19040]	1483	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
[14603]	1484	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
	1485	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
	1486
[14611]	1487	%Preallocate variable id, needed to write variables in netcdf file
[14631]	1488	var_id=zeros(1000,1);%preallocate
[14609]	1489
	1490	for step=1:2,
	1491	counter=0;
[19040]	1492	[var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
[14609]	1493	if step==1, netcdf.endDef(ncid); end
[14603]	1494	end
[14611]	1495
[14631]	1496	if counter>1000,
	1497	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]	1498	end
	1499
	1500	netcdf.close(ncid)
[14603]	1501	end % }}}
[19040]	1502	function xylim(self) % {{{
[14405]	1503
[19040]	1504	xlim([min(self.mesh.x) max(self.mesh.x)]);
	1505	ylim([min(self.mesh.y) max(self.mesh.y)])
[14405]	1506	end % }}}
[15316]	1507	function md=upload(md) % {{{
	1508	%the goal of this routine is to upload the model onto a server, and to empty it.
	1509	%So first, save the model with a unique name and upload the file to the server:
	1510	random_part=fix(rand(1)*10000);
	1511	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
	1512	eval(['save ' id ' md']);
	1513
	1514	%Now, upload the file:
	1515	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
	1516
	1517	%Now, empty this model of everything except settings, and record name of file we just uploaded!
	1518	settings_back=md.settings;
	1519	md=model();
	1520	md.settings=settings_back;
	1521	md.settings.upload_filename=id;
	1522
	1523	%get locally rid of file that was uploaded
	1524	eval(['delete ' id]);
	1525
	1526	end % }}}
	1527	function md=download(md) % {{{
[15643]	1528
[15316]	1529	%the goal of this routine is to download the internals of the current model from a server, because
	1530	%this model is empty, except for the settings which tell us where to go and find this model!
[15643]	1531
[15316]	1532	%Download the file:
	1533	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
	1534
	1535	name=md.settings.upload_filename;
	1536
	1537	%Now, load this model:
	1538	md=loadmodel(md.settings.upload_filename);
	1539
	1540	%get locally rid of file that was downloaded
	1541	eval(['delete ' name]);
	1542
	1543	end % }}}
[22955]	1544	function savemodeljs(md,modelname,websiteroot,varargin) % {{{
	1545
[19879]	1546	%the goal of this routine is to save the model as a javascript array that can be included in any html
	1547	%file:
	1548
[22955]	1549	options=pairoptions(varargin{:});
	1550	optimization=getfieldvalue(options,'optimize',0);
	1551
	1552
[19879]	1553	%disp:
[19894]	1554	disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
[19879]	1555
	1556	%open file for writing and declare the model:
[19894]	1557	fid=fopen([websiteroot '/js/' modelname '.js'],'w');
[19879]	1558	fprintf(fid,'var %s=new model();\n',modelname);
	1559
	1560	%now go through all the classes and fwrite all the corresponding fields:
	1561
	1562	fields=properties('model');
	1563	for i=1:length(fields),
	1564	field=fields{i};
	1565
	1566	%Some properties do not need to be saved
[19894]	1567	if ismember(field,{'results','cluster' }),
[19879]	1568	continue;
	1569	end
	1570
[22955]	1571	%some optimization:
	1572	if optimization==1,
	1573	%optimize for plotting only:
	1574	if ~ismember(field,{'geometry','mesh','mask'}),
	1575	continue;
	1576	end
	1577	end
	1578
[19879]	1579	%Check that current field is an object
	1580	if ~isobject(md.(field))
	1581	error(['field ''' char(field) ''' is not an object']);
	1582	end
	1583
	1584	%savemodeljs for current object
	1585	%disp(['javascript saving ' field '...']);
	1586	savemodeljs(md.(field),fid,modelname);
	1587	end
	1588
	1589	%done, close file:
	1590	fclose(fid);
	1591	end
[13692]	1592	end
[8926]	1593	end

Note: See TracBrowser for help on using the repository browser.

Download in other formats: