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source: issm/trunk-jpl/src/m/classes/model.m@ 24134

Last change on this file since 24134 was 24134, checked in by rueckamp, 6 years ago
CHG: extract function now keeps all TransientSolution time steps
File size: 69.6 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;
[19984]	24	slr = 0;
[9778]	25
[13692]	26	debug = 0;
	27	verbose = 0;
	28	settings = 0;
[14621]	29	toolkits = 0;
[13692]	30	cluster = 0;
[9778]	31
[13692]	32	balancethickness = 0;
[17757]	33	stressbalance = 0;
[13692]	34	groundingline = 0;
	35	hydrology = 0;
[17757]	36	masstransport = 0;
[13692]	37	thermal = 0;
	38	steadystate = 0;
	39	transient = 0;
[22958]	40	levelset = 0;
[18757]	41	calving = 0;
[23652]	42	frontalforcings = 0;
[22958]	43	love = 0;
	44	gia = 0;
[21260]	45	esa = 0;
[22958]	46
[13692]	47	autodiff = 0;
	48	inversion = 0;
	49	qmu = 0;
[22955]	50	amr = 0;
[13692]	51	results = 0;
[16388]	52	outputdefinition = 0;
[13692]	53	radaroverlay = 0;
	54	miscellaneous = 0;
	55	private = 0;
[9778]	56
[13692]	57	%}}}
	58	end
	59	methods (Static)
	60	function md = loadobj(md) % {{{
	61	% This function is directly called by matlab when a model object is
	62	% loaded. If the input is a struct it is an old version of model and
	63	% old fields must be recovered (make sure they are in the deprecated
	64	% model properties)
[8926]	65
[13692]	66	if verLessThan('matlab','7.9'),
	67	disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
	68	disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
[8952]	69
[13692]	70	% This is a Matlab bug: all the fields of md have their default value
	71	% Example of error message:
	72	% Warning: Error loading an object of class 'model':
	73	% Undefined function or method 'exist' for input arguments of type 'cell'
	74	%
	75	% This has been fixed in MATLAB 7.9 (R2009b) and later versions
	76	end
[8952]	77
[13692]	78	if isstruct(md)
	79	disp('Recovering model object from a previous version');
	80	md = structtomodel(model,md);
	81	end
[13239]	82
[13692]	83	%2012 August 4th
	84	if isa(md.materials,'materials'),
	85	disp('Recovering old materials');
	86	if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
[13718]	87	md.materials=matice(md.materials);
	88	else
[13692]	89	md.materials=matdamageice(md.materials);
	90	end
	91	end
[14559]	92	%2013 April 12
[15771]	93	if numel(md.stressbalance.loadingforce==1)
	94	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14559]	95	end
[14618]	96	%2013 April 17
	97	if isa(md.hydrology,'hydrology'),
	98	disp('Recovering old hydrology class');
	99	md.hydrology=hydrologyshreve(md.materials);
	100	end
[16356]	101	%2013 October 9
	102	if ~isa(md.damage,'damage'),
	103	md.damage=damage();
	104	md.damage.D=zeros(md.mesh.numberofvertices,1);
	105	md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
	106	end
[16822]	107	%2013 November 18
	108	if ~isa(md.outputdefinition,'outputdefinition'),
	109	md.outputdefinition=outputdefinition();
	110	end
[17558]	111	%2014 March 26th
	112	if isa(md.mesh,'mesh'),
[17566]	113	disp('Recovering old mesh class');
	114	if isprop(md.mesh,'dimension'),
	115	if md.mesh.dimension==2,
	116	md.mesh=mesh2d(md.mesh);
	117	else
	118	md.mesh=mesh3dprisms(md.mesh);
	119	end
[17558]	120	else
[17566]	121	md.mesh=mesh2dvertical(md.mesh);
[17558]	122	end
	123	end
[18775]	124	%2014 November 12
[21702]	125	if isa(md.calving,'double'); md.calving=calving(); end
[20059]	126	%2016 February 3
[21702]	127	if isa(md.slr,'double'); md.slr=slr(); end
[21260]	128	%2016 October 11
[21702]	129	if isa(md.esa,'double'); md.esa=esa(); end
[21545]	130	%2017 February 10th
[23434]	131	if isa(md.settings,'settings'), %this 'isa' verification: 2018 October 24th
	132	if md.settings.solver_residue_threshold==0,
	133	md.settings.solver_residue_threshold = 1e-6;
	134	end
[21545]	135	end
[21667]	136	%2017 April 10th
[21702]	137	if isa(md.gia,'gia'), md.gia=giaivins(); end
	138	%2017 May 4th
	139	if isa(md.amr,'double'); md.amr=amr(); end
[22019]	140	%2017 Aug 29th
[22040]	141	if isa(md.love,'double'); md.love=fourierlove(); end
[22194]	142	%2017 Oct 26th
	143	if isa(md.calving,'calvingdev')
	144	disp('Warning: calvingdev is now calvingvonmises');
	145	md.calving=calvingvonmises(md.calving);
	146	end
[22955]	147	%2017 Dec 21st (needs to be here)
	148	if isempty(md.settings)
	149	disp('Warning: md.settings had to be reset, make sure to adjust md.settings.output_frequency and other fields');
	150	md.settings = issmsettings();
	151	end
[23503]	152	%2018 Dec 1st
	153	if md.settings.sb_coupling_frequency==0
	154	md.settings.sb_coupling_frequency=1;
	155	end
[23652]	156	%2019 Jan..
	157	if isa(md.frontalforcings,'double');
	158	if(~isnan(md.calving.meltingrate))
	159	disp('Warning: md.calving.meltingrate is now in md.frontalforcings');
	160	end
	161	md.frontalforcings=frontalforcings(md.calving);
	162	end
[23758]	163	%2019 Feb 26
	164	if isa(md.settings.results_on_nodes,'double')
	165	if md.settings.results_on_nodes == 0
	166	md.settings.results_on_nodes = {};
	167	else
	168	md.settings.results_on_nodes = {'all'};
	169	end
	170	end
[23814]	171	%2019 Mar 28
[23984]	172	if isa(md.smb,'SMBcomponents') \| isa(md.smb,'SMBmeltcomponents') \| isa(md.smb,'SMBforcing') \| isa(md.smb,'SMBgemb')
	173	if isa(md.smb.isclimatology,'double')
	174	if prod(size(md.smb.isclimatology)) ~= 1
	175	md.smb.isclimatology = 0;
	176	end
[23814]	177	end
	178	end
[13692]	179	end% }}}
	180	end
	181	methods
	182	function md = model(varargin) % {{{
[8926]	183
[13692]	184	switch nargin
	185	case 0
	186	md=setdefaultparameters(md);
[18492]	187	case 1
[19087]	188	error('model constructor not supported yet');
[18503]	189
[13692]	190	otherwise
	191	error('model constructor error message: 0 of 1 argument only in input.');
	192	end
	193	end
	194	%}}}
	195	function md = checkmessage(md,string) % {{{
	196	if(nargout~=1) error('wrong usage, model must be an output'); end
	197	disp(['model not consistent: ' string]);
	198	md.private.isconsistent=false;
	199	end
	200	%}}}
	201	function md = collapse(md)% {{{
	202	%COLLAPSE - collapses a 3d mesh into a 2d mesh
	203	%
	204	% This routine collapses a 3d model into a 2d model
	205	% and collapses all the fileds of the 3d model by
	206	% taking their depth-averaged values
	207	%
	208	% Usage:
	209	% md=collapse(md)
	210	%
	211	% See also: EXTRUDE, MODELEXTRACT
[13005]	212
[13692]	213	%Check that the model is really a 3d model
[17687]	214	if ~strcmp(md.mesh.elementtype(),'Penta'),
[13692]	215	error('collapse error message: only 3d mesh can be collapsed')
	216	end
[13005]	217
[17724]	218	%Start with changing all the fields from the 3d mesh
[13005]	219
[21827]	220	%dealing with the friction law
[13692]	221	%drag is limited to nodes that are on the bedrock.
[18775]	222	if isa(md.friction,'friction'),
	223	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	224	md.friction.p=project2d(md,md.friction.p,1);
	225	md.friction.q=project2d(md,md.friction.q,1);
[21819]	226	elseif isa(md.friction,'frictioncoulomb'),
	227	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	228	md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1);
	229	md.friction.p=project2d(md,md.friction.p,1);
	230	md.friction.q=project2d(md,md.friction.q,1);
[18775]	231	elseif isa(md.friction,'frictionhydro'),
	232	md.friction.q=project2d(md,md.friction.q,1);
	233	md.friction.C=project2d(md,md.friction.C,1);
	234	md.friction.As=project2d(md,md.friction.As,1);
[18798]	235	md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
[18775]	236	elseif isa(md.friction,'frictionwaterlayer'),
	237	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	238	md.friction.p=project2d(md,md.friction.p,1);
	239	md.friction.q=project2d(md,md.friction.q,1);
	240	md.friction.water_layer=project2d(md,md.friction.water_layer,1);
	241	elseif isa(md.friction,'frictionweertman'),
	242	md.friction.C=project2d(md,md.friction.C,1);
	243	md.friction.m=project2d(md,md.friction.m,1);
[19720]	244	elseif isa(md.friction,'frictionweertmantemp'),
	245	md.friction.C=project2d(md,md.friction.C,1);
	246	md.friction.m=project2d(md,md.friction.m,1);
	247	else
	248	disp('friction type not supported');
[21827]	249	end
[13005]	250
[13692]	251	%observations
	252	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
	253	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
	254	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
	255	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
	256	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
	257	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
[19527]	258	if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
	259	md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
	260	elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
	261	md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
[13692]	262	end;
[13005]	263
[13692]	264	%results
	265	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
	266	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
	267	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
	268	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
[18578]	269	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[18506]	270	if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
[18578]	271	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
	272	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
	273	if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
[21417]	274	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
	275	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
[21530]	276	%giaivins
[21584]	277	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
	278	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
[15021]	279
[13692]	280	%elementstype
	281	if ~isnan(md.flowequation.element_equation)
	282	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
	283	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]	284	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
	285	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
	286	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]	287	end
[13005]	288
[13692]	289	%boundary conditions
[15771]	290	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
	291	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
	292	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
	293	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
	294	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[15767]	295	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
[21544]	296	if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
[21417]	297	if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
[13692]	298	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]	299
[18506]	300	% Hydrologydc variables
	301	if isa(md.hydrology,'hydrologydc');
	302	md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
	303	md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
	304	md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
	305	md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
	306	if(md.hydrology.isefficientlayer==1)
	307	md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
[21808]	308	end
	309	end
[18506]	310
[13692]	311	%materials
	312	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
	313	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]	314
	315	%damage:
[17940]	316	if md.damage.isdamage,
	317	md.damage.D=DepthAverage(md,md.damage.D);
	318	end
[13005]	319
[13692]	320	%special for thermal modeling:
[18378]	321	if ~isnan(md.basalforcings.groundedice_melting_rate),
	322	md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
	323	end
[21417]	324	if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
[18378]	325	md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
	326	end
[13692]	327	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]	328
[21417]	329	if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
	330	md.calving.coeff=project2d(md,md.calving.coeff,1);
	331	end
[23652]	332	if isprop(md.frontalforcings,'meltingrate') & ~isnan(md.frontalforcings.meltingrate),
	333	md.frontalforcings.meltingrate=project2d(md,md.frontalforcings.meltingrate,1);
[21417]	334	end
	335
[13692]	336	%update of connectivity matrix
	337	md.mesh.average_vertex_connectivity=25;
[13005]	338
[13692]	339	%Collapse the mesh
	340	nodes2d=md.mesh.numberofvertices2d;
	341	elements2d=md.mesh.numberofelements2d;
[13005]	342
[13692]	343	%parameters
	344	md.geometry.surface=project2d(md,md.geometry.surface,1);
	345	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
[17590]	346	md.geometry.base=project2d(md,md.geometry.base,1);
[18480]	347	if ~isnan(md.geometry.bed),
	348	md.geometry.bed=project2d(md,md.geometry.bed,1);
	349	end
[17991]	350
[18378]	351	if ~isnan(md.mask.groundedice_levelset),
	352	md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
	353	end
	354	if ~isnan(md.mask.ice_levelset),
	355	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
	356	end
[13005]	357
[22955]	358	%lat long
	359	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
	360	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
	361
[21808]	362	%outputdefinitions
	363	for i=1:length(md.outputdefinition.definitions)
	364	if isobject(md.outputdefinition.definitions{i})
	365	%get subfields
	366	solutionsubfields=fields(md.outputdefinition.definitions{i});
	367	for j=1:length(solutionsubfields),
	368	field=md.outputdefinition.definitions{i}.(solutionsubfields{j});
	369	if length(field)==md.mesh.numberofvertices \| length(field)==md.mesh.numberofelements,
	370	md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1);
	371	end
	372	end
	373	end
	374	end
	375
[13692]	376	%Initialize with the 2d mesh
[17724]	377	mesh=mesh2d();
	378	mesh.x=md.mesh.x2d;
	379	mesh.y=md.mesh.y2d;
	380	mesh.numberofvertices=md.mesh.numberofvertices2d;
	381	mesh.numberofelements=md.mesh.numberofelements2d;
	382	mesh.elements=md.mesh.elements2d;
[21499]	383	if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end
	384	if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end
	385	mesh.epsg=md.mesh.epsg;
[22324]	386	if numel(md.mesh.scale_factor)==md.mesh.numberofvertices, mesh.scale_factor=project2d(md,md.mesh.scale_factor,1); end
[17991]	387	if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
	388	if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
[17724]	389	md.mesh=mesh;
[18738]	390	md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
	391	md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
[19955]	392	md.mesh.segments=contourenvelope(md.mesh);
[13005]	393
[13692]	394	end % }}}
[22955]	395	function md2 = extract(md,area,varargin) % {{{
[13692]	396	%extract - extract a model according to an Argus contour or flag list
	397	%
	398	% This routine extracts a submodel from a bigger model with respect to a given contour
	399	% md must be followed by the corresponding exp file or flags list
	400	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
	401	% If user wants every element outside the domain to be
[15564]	402	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]	403	% an empty string '' will be considered as an empty domain
	404	% a string 'all' will be considered as the entire domain
	405	%
	406	% Usage:
	407	% md2=extract(md,area);
	408	%
	409	% Examples:
	410	% md2=extract(md,'Domain.exp');
	411	%
	412	% See also: EXTRUDE, COLLAPSE
[13005]	413
[13692]	414	%copy model
	415	md1=md;
[13005]	416
[22955]	417	%recover optoins:
	418	options=pairoptions(varargin{:});
	419
[13692]	420	%some checks
[22955]	421	if ((nargin<2) \| (nargout~=1)),
[13692]	422	help extract
	423	error('extract error message: bad usage');
	424	end
[13005]	425
[13692]	426	%get elements that are inside area
	427	flag_elem=FlagElements(md1,area);
	428	if ~any(flag_elem),
	429	error('extracted model is empty');
	430	end
[13005]	431
[13692]	432	%kick out all elements with 3 dirichlets
[22955]	433	if getfieldvalue(options,'spccheck',1)
	434	spc_elem=find(~flag_elem);
	435	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
	436	flag=ones(md1.mesh.numberofvertices,1);
	437	flag(spc_node)=0;
	438	pos=find(sum(flag(md1.mesh.elements),2)==0);
	439	flag_elem(pos)=0;
	440	end
[13005]	441
[13692]	442	%extracted elements and nodes lists
	443	pos_elem=find(flag_elem);
	444	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]	445
[13692]	446	%keep track of some fields
	447	numberofvertices1=md1.mesh.numberofvertices;
	448	numberofelements1=md1.mesh.numberofelements;
	449	numberofvertices2=length(pos_node);
	450	numberofelements2=length(pos_elem);
	451	flag_node=zeros(numberofvertices1,1);
	452	flag_node(pos_node)=1;
[13005]	453
[13692]	454	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
	455	Pelem=zeros(numberofelements1,1);
	456	Pelem(pos_elem)=[1:numberofelements2]';
	457	Pnode=zeros(numberofvertices1,1);
	458	Pnode(pos_node)=[1:numberofvertices2]';
[13005]	459
[13857]	460	%renumber the elements (some nodes won't exist anymore)
[13692]	461	elements_1=md1.mesh.elements;
	462	elements_2=elements_1(pos_elem,:);
	463	elements_2(:,1)=Pnode(elements_2(:,1));
	464	elements_2(:,2)=Pnode(elements_2(:,2));
	465	elements_2(:,3)=Pnode(elements_2(:,3));
[17558]	466	if isa(md1.mesh,'mesh3dprisms'),
[13692]	467	elements_2(:,4)=Pnode(elements_2(:,4));
	468	elements_2(:,5)=Pnode(elements_2(:,5));
	469	elements_2(:,6)=Pnode(elements_2(:,6));
	470	end
[13005]	471
[13857]	472	%OK, now create the new model!
[13005]	473
[13857]	474	%take every field from model
[13692]	475	md2=md1;
[13005]	476
[13692]	477	%automatically modify fields
[13005]	478
[13692]	479	%loop over model fields
	480	model_fields=fields(md1);
	481	for i=1:length(model_fields),
	482	%get field
	483	field=md1.(model_fields{i});
	484	fieldsize=size(field);
	485	if isobject(field), %recursive call
	486	object_fields=fields(md1.(model_fields{i}));
	487	for j=1:length(object_fields),
	488	%get field
	489	field=md1.(model_fields{i}).(object_fields{j});
	490	fieldsize=size(field);
	491	%size = number of nodes * n
	492	if fieldsize(1)==numberofvertices1
	493	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
	494	elseif (fieldsize(1)==numberofvertices1+1)
	495	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]	496	%size = number of elements * n
[13692]	497	elseif fieldsize(1)==numberofelements1
	498	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
[21428]	499	elseif (fieldsize(1)==numberofelements1+1)
	500	md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
[13692]	501	end
	502	end
	503	else
	504	%size = number of nodes * n
	505	if fieldsize(1)==numberofvertices1
	506	md2.(model_fields{i})=field(pos_node,:);
	507	elseif (fieldsize(1)==numberofvertices1+1)
	508	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]	509	%size = number of elements * n
[13692]	510	elseif fieldsize(1)==numberofelements1
	511	md2.(model_fields{i})=field(pos_elem,:);
[21428]	512	elseif (fieldsize(1)==numberofelements1+1)
	513	md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
[13692]	514	end
	515	end
	516	end
[13005]	517
[13692]	518	%modify some specific fields
[13005]	519
[13692]	520	%Mesh
	521	md2.mesh.numberofelements=numberofelements2;
	522	md2.mesh.numberofvertices=numberofvertices2;
	523	md2.mesh.elements=elements_2;
[13005]	524
[13692]	525	%mesh.uppervertex mesh.lowervertex
[17558]	526	if isa(md1.mesh,'mesh3dprisms'),
[13692]	527	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
	528	pos=find(~isnan(md2.mesh.uppervertex));
	529	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]	530
[13692]	531	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
	532	pos=find(~isnan(md2.mesh.lowervertex));
	533	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]	534
[13692]	535	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
	536	pos=find(~isnan(md2.mesh.upperelements));
	537	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]	538
[13692]	539	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
	540	pos=find(~isnan(md2.mesh.lowerelements));
	541	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
	542	end
[13005]	543
[13692]	544	%Initial 2d mesh
[17558]	545	if isa(md1.mesh,'mesh3dprisms'),
[13692]	546	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
	547	pos_elem_2d=find(flag_elem_2d);
	548	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
	549	pos_node_2d=find(flag_node_2d);
[13005]	550
[13692]	551	md2.mesh.numberofelements2d=length(pos_elem_2d);
	552	md2.mesh.numberofvertices2d=length(pos_node_2d);
	553	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
	554	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
	555	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
	556	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]	557
[13692]	558	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
	559	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
	560	end
[13005]	561
[13692]	562	%Edges
[17686]	563	if(dimension(md.mesh)==2),
[17563]	564	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
	565	%renumber first two columns
	566	pos=find(md2.mesh.edges(:,4)~=-1);
	567	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
	568	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
	569	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
	570	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
	571	%remove edges when the 2 vertices are not in the domain.
	572	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
	573	%Replace all zeros by -1 in the last two columns
	574	pos=find(md2.mesh.edges(:,3)==0);
	575	md2.mesh.edges(pos,3)=-1;
	576	pos=find(md2.mesh.edges(:,4)==0);
	577	md2.mesh.edges(pos,4)=-1;
	578	%Invert -1 on the third column with last column (Also invert first two columns!!)
	579	pos=find(md2.mesh.edges(:,3)==-1);
	580	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
	581	md2.mesh.edges(pos,4)=-1;
	582	values=md2.mesh.edges(pos,2);
	583	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
	584	md2.mesh.edges(pos,1)=values;
	585	%Finally remove edges that do not belong to any element
	586	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
	587	md2.mesh.edges(pos,:)=[];
	588	end
[13692]	589	end
[13005]	590
[13692]	591	%Penalties
[15771]	592	if ~isnan(md2.stressbalance.vertex_pairing),
	593	for i=1:size(md1.stressbalance.vertex_pairing,1);
	594	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]	595	end
[15771]	596	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]	597	end
[15767]	598	if ~isnan(md2.masstransport.vertex_pairing),
	599	for i=1:size(md1.masstransport.vertex_pairing,1);
	600	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]	601	end
[15767]	602	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]	603	end
[13005]	604
[13692]	605	%recreate segments
[20322]	606	if isa(md1.mesh,'mesh2d') \| isa(md1.mesh','mesh3dsurface'),
[13692]	607	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	608	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
[19957]	609	md2.mesh.segments=contourenvelope(md2.mesh);
[13692]	610	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
	611	else
	612	%First do the connectivity for the contourenvelope in 2d
	613	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
	614	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
[19957]	615	segments=contourenvelope(md2.mesh);
[17565]	616	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
[13692]	617	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
	618	%Then do it for 3d as usual
	619	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	620	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	621	end
[13005]	622
[13692]	623	%Boundary conditions: Dirichlets on new boundary
	624	%Catch the elements that have not been extracted
	625	orphans_elem=find(~flag_elem);
	626	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
	627	%Figure out which node are on the boundary between md2 and md1
	628	nodestoflag1=intersect(orphans_node,pos_node);
	629	nodestoflag2=Pnode(nodestoflag1);
[23771]	630	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>1 & numel(md1.stressbalance.spcvz)>1,
[13692]	631	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]	632	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
	633	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]	634	else
[15771]	635	md2.stressbalance.spcvx(nodestoflag2)=NaN;
	636	md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]	637	disp(' ')
	638	disp('!! extract warning: spc values should be checked !!')
	639	disp(' ')
	640	end
	641	%put 0 for vz
[15771]	642	md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]	643	end
	644	if ~isnan(md1.thermal.spctemperature),
	645	md2.thermal.spctemperature(nodestoflag2,1)=1;
	646	end
[13005]	647
[13692]	648	%Results fields
	649	if isstruct(md1.results),
	650	md2.results=struct();
	651	solutionfields=fields(md1.results);
	652	for i=1:length(solutionfields),
[14230]	653	if isstruct(md1.results.(solutionfields{i}))
	654	%get subfields
[24134]	655	% loop over time steps
	656	for p=1:length(md1.results.(solutionfields{i}))
	657	current = md1.results.(solutionfields{i})(p);
	658	solutionsubfields=fields(current);
	659	for j=1:length(solutionsubfields),
	660	field=md1.results.(solutionfields{i})(p).(solutionsubfields{j});
[14230]	661	if length(field)==numberofvertices1,
[24134]	662	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_node);
[14230]	663	elseif length(field)==numberofelements1,
[24134]	664	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_elem);
[14230]	665	else
[24134]	666	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field;
[14230]	667	end
[24134]	668	end
[14230]	669	end
	670	else
	671	field=md1.results.(solutionfields{i});
[13692]	672	if length(field)==numberofvertices1,
[14230]	673	md2.results.(solutionfields{i})=field(pos_node);
[13692]	674	elseif length(field)==numberofelements1,
[14230]	675	md2.results.(solutionfields{i})=field(pos_elem);
[13692]	676	else
[14230]	677	md2.results.(solutionfields{i})=field;
[13692]	678	end
	679	end
	680	end
	681	end
[13005]	682
[21808]	683	%OutputDefinitions fields
	684	for i=1:length(md1.outputdefinition.definitions),
	685	if isobject(md1.outputdefinition.definitions{i})
	686	%get subfields
	687	solutionsubfields=fields(md1.outputdefinition.definitions{i});
	688	for j=1:length(solutionsubfields),
	689	field=md1.outputdefinition.definitions{i}.(solutionsubfields{j});
	690	if length(field)==numberofvertices1,
	691	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node);
	692	elseif length(field)==numberofelements1,
	693	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem);
	694	end
	695	end
	696	end
	697	end
	698
[13692]	699	%Keep track of pos_node and pos_elem
	700	md2.mesh.extractedvertices=pos_node;
	701	md2.mesh.extractedelements=pos_elem;
	702	end % }}}
	703	function md = extrude(md,varargin) % {{{
	704	%EXTRUDE - vertically extrude a 2d mesh
	705	%
	706	% vertically extrude a 2d mesh and create corresponding 3d mesh.
	707	% The vertical distribution can:
	708	% - follow a polynomial law
	709	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
	710	% - be discribed by a list of coefficients (between 0 and 1)
	711	%
	712	%
	713	% Usage:
	714	% md=extrude(md,numlayers,extrusionexponent);
	715	% md=extrude(md,numlayers,lowerexponent,upperexponent);
	716	% md=extrude(md,listofcoefficients);
	717	%
	718	% Example:
[18216]	719	% md=extrude(md,15,1.3);
	720	% md=extrude(md,15,1.3,1.2);
[13692]	721	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
	722	%
	723	% See also: MODELEXTRACT, COLLAPSE
[13005]	724
[13692]	725	%some checks on list of arguments
	726	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
	727	help extrude;
	728	error('extrude error message');
	729	end
[13005]	730
[13692]	731	%Extrude the mesh
	732	if nargin==2, %list of coefficients
	733	clist=varargin{1};
	734	if any(clist<0) \| any(clist>1),
	735	error('extrusioncoefficients must be between 0 and 1');
	736	end
	737	extrusionlist=sort(unique([clist(:);0;1]));
	738	numlayers=length(extrusionlist);
	739	elseif nargin==3, %one polynomial law
	740	if varargin{2}<=0,
	741	help extrude;
	742	error('extrusionexponent must be >=0');
	743	end
	744	numlayers=varargin{1};
	745	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
	746	elseif nargin==4, %two polynomial laws
	747	numlayers=varargin{1};
	748	lowerexp=varargin{2};
	749	upperexp=varargin{3};
[13005]	750
[13692]	751	if varargin{2}<=0 \| varargin{3}<=0,
	752	help extrude;
	753	error('lower and upper extrusionexponents must be >=0');
	754	end
[13005]	755
[13692]	756	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
	757	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
	758	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]	759
[13692]	760	end
[13005]	761
[13692]	762	if numlayers<2,
	763	error('number of layers should be at least 2');
	764	end
[17686]	765	if strcmp(md.mesh.domaintype(),'3D')
[13692]	766	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
	767	end
[13005]	768
[13692]	769	%Initialize with the 2d mesh
[17558]	770	mesh2d = md.mesh;
	771	md.mesh=mesh3dprisms();
	772	md.mesh.x = mesh2d.x;
	773	md.mesh.y = mesh2d.y;
	774	md.mesh.elements = mesh2d.elements;
	775	md.mesh.numberofelements = mesh2d.numberofelements;
	776	md.mesh.numberofvertices = mesh2d.numberofvertices;
	777
	778	md.mesh.lat = mesh2d.lat;
	779	md.mesh.long = mesh2d.long;
[18558]	780	md.mesh.epsg = mesh2d.epsg;
[22324]	781	md.mesh.scale_factor = mesh2d.scale_factor;
[17558]	782
	783	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
	784	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
	785	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
	786	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
	787
	788	md.mesh.extractedvertices = mesh2d.extractedvertices;
	789	md.mesh.extractedelements = mesh2d.extractedelements;
	790
[13692]	791	x3d=[];
	792	y3d=[];
	793	z3d=[]; %the lower node is on the bed
	794	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
[17590]	795	bed3d=md.geometry.base;
[13005]	796
[13692]	797	%Create the new layers
	798	for i=1:numlayers,
	799	x3d=[x3d; md.mesh.x];
	800	y3d=[y3d; md.mesh.y];
	801	%nodes are distributed between bed and surface accordingly to the given exponent
	802	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
	803	end
	804	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	805
[13692]	806	%Extrude elements
	807	elements3d=[];
	808	for i=1:numlayers-1,
	809	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
	810	end
	811	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	812
[13692]	813	%Keep a trace of lower and upper nodes
[17590]	814	lowervertex=NaN*ones(number_nodes3d,1);
	815	uppervertex=NaN*ones(number_nodes3d,1);
	816	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
	817	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
	818	md.mesh.lowervertex=lowervertex;
	819	md.mesh.uppervertex=uppervertex;
[13005]	820
[13692]	821	%same for lower and upper elements
[17590]	822	lowerelements=NaN*ones(number_el3d,1);
	823	upperelements=NaN*ones(number_el3d,1);
	824	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
	825	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
	826	md.mesh.lowerelements=lowerelements;
	827	md.mesh.upperelements=upperelements;
[13005]	828
[13692]	829	%Save old mesh
	830	md.mesh.x2d=md.mesh.x;
	831	md.mesh.y2d=md.mesh.y;
	832	md.mesh.elements2d=md.mesh.elements;
	833	md.mesh.numberofelements2d=md.mesh.numberofelements;
	834	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]	835
[13692]	836	%Build global 3d mesh
	837	md.mesh.elements=elements3d;
	838	md.mesh.x=x3d;
	839	md.mesh.y=y3d;
	840	md.mesh.z=z3d;
	841	md.mesh.numberofelements=number_el3d;
	842	md.mesh.numberofvertices=number_nodes3d;
	843	md.mesh.numberoflayers=numlayers;
[13005]	844
[13692]	845	%Ok, now deal with the other fields from the 2d mesh:
[13005]	846
[19048]	847	%bedinfo and surface info
	848	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
	849	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
	850	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
	851
[13692]	852	%lat long
	853	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
	854	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[22324]	855	md.mesh.scale_factor=project3d(md,'vector',md.mesh.scale_factor,'type','node');
[13005]	856
[19048]	857	md.geometry=extrude(md.geometry,md);
	858	md.friction = extrude(md.friction,md);
	859	md.inversion = extrude(md.inversion,md);
[19527]	860	md.smb = extrude(md.smb,md);
[19048]	861	md.initialization = extrude(md.initialization,md);
[13005]	862
[19050]	863	md.flowequation=md.flowequation.extrude(md);
[19048]	864	md.stressbalance=extrude(md.stressbalance,md);
[19050]	865	md.thermal=md.thermal.extrude(md);
	866	md.masstransport=md.masstransport.extrude(md);
[20460]	867	md.levelset=extrude(md.levelset,md);
[19048]	868	md.calving=extrude(md.calving,md);
[23652]	869	md.frontalforcings=extrude(md.frontalforcings,md);
[19048]	870	md.hydrology = extrude(md.hydrology,md);
[22955]	871	md.slr = extrude(md.slr,md);
[13005]	872
[13692]	873	%connectivity
[17991]	874	if ~isnan(md.mesh.elementconnectivity)
	875	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
	876	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
	877	for i=2:numlayers-1,
	878	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
	879	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
	880	end
	881	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13692]	882	end
[13005]	883
[19048]	884	md.materials=extrude(md.materials,md);
	885	md.damage=extrude(md.damage,md);
	886	md.mask=extrude(md.mask,md);
	887	md.qmu=extrude(md.qmu,md);
	888	md.basalforcings=extrude(md.basalforcings,md);
[21808]	889	md.outputdefinition=extrude(md.outputdefinition,md);
[13005]	890
[13692]	891	%increase connectivity if less than 25:
	892	if md.mesh.average_vertex_connectivity<=25,
	893	md.mesh.average_vertex_connectivity=100;
	894	end
[13005]	895	end % }}}
[13692]	896	function md = structtomodel(md,structmd) % {{{
[8952]	897
[13692]	898	if ~isstruct(structmd) error('input model is not a structure'); end
[8952]	899
[13692]	900	%loaded model is a struct, initialize output and recover all fields
	901	md = structtoobj(model,structmd);
[8952]	902
[13692]	903	%Old field now classes
	904	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
	905	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]	906
[13692]	907	%Field name change
	908	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	909	if isfield(structmd,'p'), md.friction.p=structmd.p; end
	910	if isfield(structmd,'q'), md.friction.q=structmd.p; end
[18378]	911	if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
[18068]	912	if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
[18378]	913	if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
[19527]	914	if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
[13692]	915	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
	916	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
	917	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
	918	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
[17610]	919	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
[13692]	920	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
	921	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
	922	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]	923	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]	924	if isfield(structmd,'g'), md.constants.g=structmd.g; end
	925	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
[19527]	926	if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
[18068]	927	if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
[13692]	928	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
	929	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	930	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
	931	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
	932	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
	933	if isfield(structmd,'riftproperties'), %old implementation
	934	md.rifts=rifts();
	935	md.rifts.riftproperties=structmd.riftproperties;
	936	md.rifts.riftstruct=structmd.rifts;
	937	md.rifts.riftproperties=structmd.riftinfo;
	938	end
	939	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
	940	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
	941	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
	942	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
	943	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
	944	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
	945	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
	946	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
	947	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
	948	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
	949	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
	950	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
	951	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
	952	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
	953	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
	954	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
	955	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
	956	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
	957	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
	958	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
	959	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
	960	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]	961	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
	962	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
	963	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
	964	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
	965	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]	966	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
	967	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
	968	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
	969	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]	970	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]	971	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
	972	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
	973	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]	974	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
	975	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]	976	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
	977	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
	978	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
	979	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]	980	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]	981	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]	982	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
	983	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
	984	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
	985	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
	986	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
	987	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
	988	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
	989	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
	990	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
	991	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
	992	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
	993	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
	994	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
	995	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
	996	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
	997	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
	998	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
	999	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
	1000	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
	1001	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
[17590]	1002	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
[13692]	1003	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
[17590]	1004	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
[13692]	1005	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
	1006	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
	1007	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
	1008	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
	1009	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
	1010	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
	1011	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
[22324]	1012	if isfield(structmd,'scale_factor'), md.mesh.scale_factor=structmd.scale_factor; end
[13692]	1013	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
	1014	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
	1015	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
	1016	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
	1017	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
	1018	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
	1019	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
	1020	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
	1021	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
	1022	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
	1023	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
	1024	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
	1025	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
	1026	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
	1027	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
	1028	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
[17610]	1029	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
[13692]	1030	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
	1031	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
	1032	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
	1033	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]	1034	if isfield(structmd,'edges'),
	1035	md.mesh.edges=structmd.edges;
	1036	md.mesh.edges(isnan(md.mesh.edges))=-1;
	1037	end
[13692]	1038	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
	1039	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
	1040	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
[15771]	1041	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]	1042	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
	1043	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]	1044
[13692]	1045	if isnumeric(md.verbose),
	1046	md.verbose=verbose;
	1047	end
[15768]	1048
[13692]	1049	if isfield(structmd,'spcvelocity'),
[15771]	1050	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1051	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1052	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1053	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
	1054	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
	1055	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]	1056	end
	1057	if isfield(structmd,'spcvx'),
[15771]	1058	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1059	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]	1060	end
	1061	if isfield(structmd,'spcvy'),
[15771]	1062	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1063	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]	1064	end
	1065	if isfield(structmd,'spcvz'),
[15771]	1066	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1067	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]	1068	end
[14620]	1069	if isfield(structmd,'pressureload'),
	1070	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]	1071	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
	1072	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
	1073	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]	1074	end
[13692]	1075	end
	1076	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
	1077	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
	1078	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
	1079	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
	1080	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
	1081	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
	1082	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
	1083	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
	1084	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
	1085	end
	1086	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
	1087	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
	1088	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
	1089	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
	1090	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
	1091	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
	1092	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
	1093	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
	1094	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
	1095	end
	1096	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
	1097	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
	1098	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
	1099	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
	1100	end
	1101	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
	1102	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
[17941]	1103	if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
[13692]	1104	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
	1105	end
	1106	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
	1107	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
	1108	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
	1109	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
	1110	end
	1111	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
	1112	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
	1113	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
	1114	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
	1115	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
	1116	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
	1117	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
	1118	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
	1119	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
	1120	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
	1121	end
[11659]	1122
[13692]	1123	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
	1124	md.thermal.stabilization=2;
[15767]	1125	md.masstransport.stabilization=1;
[13692]	1126	md.balancethickness.stabilization=1;
	1127	end
[15767]	1128	if isnumeric(md.masstransport.hydrostatic_adjustment)
	1129	if md.masstransport.hydrostatic_adjustment==269,
	1130	md.masstransport.hydrostatic_adjustment='Incremental';
[13692]	1131	else
[15767]	1132	md.masstransport.hydrostatic_adjustment='Absolute';
[13692]	1133	end
	1134	end
[8952]	1135
[13692]	1136	%New fields
[19124]	1137	if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1138	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
	1139	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
	1140	end
[19124]	1141	if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1142	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
	1143	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
	1144	end
	1145	if ~isfield(structmd,'diagnostic_ref');
[15771]	1146	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]	1147	end
[14529]	1148	if ~isfield(structmd,'loadingforce');
[15771]	1149	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]	1150	end
[15768]	1151
	1152	%2013 August 9
	1153	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
	1154	disp('Recovering old prognostic class');
	1155	md.masstransport=masstransport(structmd.prognostic);
	1156	end
[15771]	1157	%2013 August 9
[15775]	1158	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
[15771]	1159	disp('Recovering old diagnostic class');
[15775]	1160	md.stressbalance=stressbalance(structmd.diagnostic);
[15771]	1161	end
[19642]	1162	%2014 January 9th
[21148]	1163	if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
[19642]	1164	disp('Recovering old surfaceforcings class');
	1165	mass_balance=structmd.surfaceforcings.mass_balance;
	1166	md.smb=SMB();
	1167	md.smb.mass_balance=mass_balance;
	1168	end
	1169	%2015 September 10
[21148]	1170	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
[19642]	1171	disp('Recovering old SMB class');
	1172	md.smb=SMBforcing(structmd.surfaceforcings);
	1173	end
[21148]	1174	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
	1175	disp('Recovering old SMBhenning class');
	1176	md.smb=SMBhenning(structmd.surfaceforcings);
	1177	end
[13692]	1178	end% }}}
	1179	function md = setdefaultparameters(md) % {{{
[8926]	1180
[13692]	1181	%initialize subclasses
[17558]	1182	md.mesh = mesh2d();
[13692]	1183	md.mask = mask();
	1184	md.constants = constants();
	1185	md.geometry = geometry();
	1186	md.initialization = initialization();
[19527]	1187	md.smb = SMBforcing();
[13692]	1188	md.basalforcings = basalforcings();
	1189	md.friction = friction();
	1190	md.rifts = rifts();
[19984]	1191	md.slr = slr();
[13692]	1192	md.timestepping = timestepping();
	1193	md.groundingline = groundingline();
	1194	md.materials = matice();
[16160]	1195	md.damage = damage();
[13692]	1196	md.flowequation = flowequation();
	1197	md.debug = debug();
[14558]	1198	md.verbose = verbose();
[22296]	1199	md.settings = issmsettings();
[17932]	1200	md.toolkits = toolkits();
[13692]	1201	md.cluster = generic();
	1202	md.balancethickness = balancethickness();
[17079]	1203	md.stressbalance = stressbalance();
[14555]	1204	md.hydrology = hydrologyshreve();
[17079]	1205	md.masstransport = masstransport();
[13692]	1206	md.thermal = thermal();
	1207	md.steadystate = steadystate();
	1208	md.transient = transient();
[22040]	1209	md.levelset = levelset();
[18757]	1210	md.calving = calving();
[23652]	1211	md.frontalforcings = frontalforcings();
[22955]	1212	md.gia = giaivins();
	1213	md.esa = esa();
[22040]	1214	md.love = fourierlove();
[21260]	1215	md.esa = esa();
[13692]	1216	md.autodiff = autodiff();
	1217	md.inversion = inversion();
	1218	md.qmu = qmu();
[22955]	1219	md.amr = amr();
[13692]	1220	md.radaroverlay = radaroverlay();
	1221	md.results = struct();
[16388]	1222	md.outputdefinition = outputdefinition();
[13692]	1223	md.miscellaneous = miscellaneous();
	1224	md.private = private();
	1225	end
	1226	%}}}
[17483]	1227	function md = tetras(md,varargin) % {{{
	1228	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
	1229	%
	1230	% Usage:
	1231	% md=tetra(md)
	1232
	1233	if ~isa(md.mesh,'mesh3dprisms')
	1234	error('mesh is not a 3d prismatic mesh');
	1235	end
	1236
	1237	%Initialize tetra mesh
	1238	md.mesh=mesh3dtetras(md.mesh);
	1239
[17754]	1240	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
	1241	steiner = 0;
	1242	nbv = md.mesh.numberofvertices;
	1243	nbt = 3*md.mesh.numberofelements;
	1244	elements = zeros(nbt,4);
	1245	for i=1:md.mesh.numberofelements
	1246	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
	1247	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
	1248	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1249	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1250	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1251	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1252	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1253	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1254	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
	1255	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
	1256	elements(end+1,:) = [v2 v3 v5 v7];
	1257	elements(end+1,:) = [v3 v5 v6 v7];
	1258	elements(end+1,:) = [v1 v3 v6 v7];
	1259	elements(end+1,:) = [v1 v4 v6 v7];
	1260	elements(end+1,:) = [v4 v5 v6 v7];
	1261	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1262	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
	1263	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1264	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1265	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1266	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1267	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
	1268	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1269	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1270	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1271	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1272	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
[18142]	1273	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
[17754]	1274	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1275	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1276	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
	1277	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1278	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1279	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
	1280	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1281	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1282	elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
	1283	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1284	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1285	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1286	elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
	1287	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1288	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
	1289	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1290	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1291	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1292	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1293	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1294	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1295	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
	1296	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
	1297	elements(end+1,:) = [v2 v5 v6 v7];
	1298	elements(end+1,:) = [v2 v3 v6 v7];
	1299	elements(end+1,:) = [v3 v4 v6 v7];
	1300	elements(end+1,:) = [v1 v3 v4 v7];
	1301	elements(end+1,:) = [v4 v5 v6 v7];
	1302	else
	1303	error('Case not supported'); %not supposed to happen!
	1304	end
[17774]	1305	%Reorder elements to make sure they are direct
	1306	for j=1:3
	1307	element = elements(3*(i-1)+j,:);
	1308	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
	1309	if det(matrix)>0,
	1310	elements(3*(i-1)+j,1)=element(2);
	1311	elements(3*(i-1)+j,2)=element(1);
	1312	end
	1313	end
[17754]	1314	end
	1315	%%Split in 3 tetras
	1316	%subelement1 = [1 2 3 5];
	1317	%subelement2 = [4 6 5 1];
	1318	%subelement3 = [5 6 3 1];
	1319	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
[17774]	1320	if steiner==0,
	1321	disp('No Steiner point required to split prismatic mesh into tets');
	1322	else
	1323	disp([num2str(steiner) ' Steiner points had to be included'])
	1324	error('Steiner point not supported yet');
	1325	end
[17754]	1326
[17483]	1327	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
	1328
	1329	md.mesh.elements=elements;
	1330	md.mesh.numberofelements=size(elements,1);
	1331
	1332	%p and q (same deal, except for element that are on the bedrock: )
[17774]	1333	if ~isnan(md.friction.p),
	1334	md.friction.p=md.friction.p(pos_elements);
	1335	md.friction.q=md.friction.q(pos_elements);
	1336	end
[17483]	1337
	1338	%elementstype
	1339	if ~isnan(md.flowequation.element_equation)
	1340	oldelements_type=md.flowequation.element_equation;
	1341	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
	1342	end
	1343
	1344	%connectivity
	1345	md.mesh.elementconnectivity=NaN;
	1346
	1347	%materials
[17774]	1348	if ~isnan(md.materials.rheology_n),
	1349	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
	1350	end
[17483]	1351
	1352	%increase connectivity if less than 25:
	1353	if md.mesh.average_vertex_connectivity<=25,
	1354	md.mesh.average_vertex_connectivity=100;
	1355	end
	1356	end % }}}
[19040]	1357	function disp(self) % {{{
	1358	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
	1359	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
	1360	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
	1361	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
[19527]	1362	disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
[19040]	1363	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
	1364	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
	1365	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
	1366	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
	1367	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
	1368	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
	1369	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
	1370	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
[19984]	1371	disp(sprintf('%19s: %-22s -- %s','slr' ,['[1x1 ' class(self.slr) ']'],'slr forcings'));
[19040]	1372	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
	1373	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
	1374	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
	1375	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
	1376	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
	1377	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
	1378	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
	1379	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
	1380	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
	1381	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
	1382	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
	1383	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
	1384	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
[21544]	1385	disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
[19040]	1386	disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
[23652]	1387	disp(sprintf('%19s: %-22s -- %s','frontalforcings' ,['[1x1 ' class(self.frontalforcings) ']'],'parameters for frontalforcings'));
[22955]	1388	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
[21260]	1389	disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
[22955]	1390	disp(sprintf('%19s: %-22s -- %s','love' ,['[1x1 ' class(self.love) ']'],'parameters for love solution'));
[19040]	1391	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
	1392	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
	1393	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
[21674]	1394	disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
[19040]	1395	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
	1396	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
	1397	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
	1398	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
[13692]	1399	end % }}}
[19040]	1400	function memory(self) % {{{
[15106]	1401
[14611]	1402	disp(sprintf('\nMemory imprint:\n'));
[14307]	1403
[14603]	1404	fields=properties('model');
	1405	mem=0;
[15106]	1406
[14603]	1407	for i=1:length(fields),
[19040]	1408	field=self.(fields{i});
[14603]	1409	s=whos('field');
	1410	mem=mem+s.bytes/1e6;
[14611]	1411	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]	1412	end
[14603]	1413	disp(sprintf('%19s--%10s','--------------','--------------'));
	1414	disp(sprintf('%19s: %g Mb','Total',mem));
[14307]	1415	end % }}}
[19040]	1416	function netcdf(self,filename) % {{{
[14603]	1417	%NETCDF - save model as netcdf
	1418	%
	1419	% Usage:
	1420	% netcdf(md,filename)
	1421	%
	1422	% Example:
	1423	% netcdf(md,'model.nc');
	1424
	1425	disp('Saving model as NetCDF');
	1426	%1. Create NetCDF file
	1427	ncid=netcdf.create(filename,'CLOBBER');
	1428	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[19040]	1429	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
[14603]	1430	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
	1431	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
	1432
[14611]	1433	%Preallocate variable id, needed to write variables in netcdf file
[14631]	1434	var_id=zeros(1000,1);%preallocate
[14609]	1435
	1436	for step=1:2,
	1437	counter=0;
[19040]	1438	[var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
[14609]	1439	if step==1, netcdf.endDef(ncid); end
[14603]	1440	end
[14611]	1441
[14631]	1442	if counter>1000,
	1443	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]	1444	end
	1445
	1446	netcdf.close(ncid)
[14603]	1447	end % }}}
[19040]	1448	function xylim(self) % {{{
[14405]	1449
[19040]	1450	xlim([min(self.mesh.x) max(self.mesh.x)]);
	1451	ylim([min(self.mesh.y) max(self.mesh.y)])
[14405]	1452	end % }}}
[15316]	1453	function md=upload(md) % {{{
	1454	%the goal of this routine is to upload the model onto a server, and to empty it.
	1455	%So first, save the model with a unique name and upload the file to the server:
	1456	random_part=fix(rand(1)*10000);
	1457	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
	1458	eval(['save ' id ' md']);
	1459
	1460	%Now, upload the file:
	1461	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
	1462
	1463	%Now, empty this model of everything except settings, and record name of file we just uploaded!
	1464	settings_back=md.settings;
	1465	md=model();
	1466	md.settings=settings_back;
	1467	md.settings.upload_filename=id;
	1468
	1469	%get locally rid of file that was uploaded
	1470	eval(['delete ' id]);
	1471
	1472	end % }}}
	1473	function md=download(md) % {{{
[15643]	1474
[15316]	1475	%the goal of this routine is to download the internals of the current model from a server, because
	1476	%this model is empty, except for the settings which tell us where to go and find this model!
[15643]	1477
[15316]	1478	%Download the file:
	1479	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
	1480
	1481	name=md.settings.upload_filename;
	1482
	1483	%Now, load this model:
	1484	md=loadmodel(md.settings.upload_filename);
	1485
	1486	%get locally rid of file that was downloaded
	1487	eval(['delete ' name]);
	1488
	1489	end % }}}
[22955]	1490	function savemodeljs(md,modelname,websiteroot,varargin) % {{{
	1491
[19879]	1492	%the goal of this routine is to save the model as a javascript array that can be included in any html
	1493	%file:
	1494
[22955]	1495	options=pairoptions(varargin{:});
	1496	optimization=getfieldvalue(options,'optimize',0);
	1497
	1498
[19879]	1499	%disp:
[19894]	1500	disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
[19879]	1501
	1502	%open file for writing and declare the model:
[19894]	1503	fid=fopen([websiteroot '/js/' modelname '.js'],'w');
[19879]	1504	fprintf(fid,'var %s=new model();\n',modelname);
	1505
	1506	%now go through all the classes and fwrite all the corresponding fields:
	1507
	1508	fields=properties('model');
	1509	for i=1:length(fields),
	1510	field=fields{i};
	1511
	1512	%Some properties do not need to be saved
[19894]	1513	if ismember(field,{'results','cluster' }),
[19879]	1514	continue;
	1515	end
	1516
[22955]	1517	%some optimization:
	1518	if optimization==1,
	1519	%optimize for plotting only:
	1520	if ~ismember(field,{'geometry','mesh','mask'}),
	1521	continue;
	1522	end
	1523	end
	1524
[19879]	1525	%Check that current field is an object
	1526	if ~isobject(md.(field))
	1527	error(['field ''' char(field) ''' is not an object']);
	1528	end
	1529
	1530	%savemodeljs for current object
	1531	%disp(['javascript saving ' field '...']);
	1532	savemodeljs(md.(field),fid,modelname);
	1533	end
	1534
	1535	%done, close file:
	1536	fclose(fid);
	1537	end
[13692]	1538	end
[8926]	1539	end

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