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source: issm/trunk-jpl/src/m/classes/model.m@ 23652

Last change on this file since 23652 was 23652, checked in by youngmc3, 6 years ago
NEW: add new class md.frontalforcings
File size: 68.9 KB

Rev	Line
[8926]	1	%MODEL class definition
	2	%
	3	% Usage:
	4	% md = model(varargin)
	5
	6	classdef model
[13692]	7	properties (SetAccess=public) %Model fields
	8	% {{{
	9	%Careful here: no other class should be used as default value this is a bug of matlab
	10	mesh = 0;
	11	mask = 0;
[9778]	12
[13692]	13	geometry = 0;
	14	constants = 0;
[19527]	15	smb = 0;
[13692]	16	basalforcings = 0;
	17	materials = 0;
[16160]	18	damage = 0;
[13692]	19	friction = 0;
	20	flowequation = 0;
	21	timestepping = 0;
	22	initialization = 0;
	23	rifts = 0;
[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
[13692]	163	end% }}}
	164	end
	165	methods
	166	function md = model(varargin) % {{{
[8926]	167
[13692]	168	switch nargin
	169	case 0
	170	md=setdefaultparameters(md);
[18492]	171	case 1
[19087]	172	error('model constructor not supported yet');
[18503]	173
[13692]	174	otherwise
	175	error('model constructor error message: 0 of 1 argument only in input.');
	176	end
	177	end
	178	%}}}
	179	function md = checkmessage(md,string) % {{{
	180	if(nargout~=1) error('wrong usage, model must be an output'); end
	181	disp(['model not consistent: ' string]);
	182	md.private.isconsistent=false;
	183	end
	184	%}}}
	185	function md = collapse(md)% {{{
	186	%COLLAPSE - collapses a 3d mesh into a 2d mesh
	187	%
	188	% This routine collapses a 3d model into a 2d model
	189	% and collapses all the fileds of the 3d model by
	190	% taking their depth-averaged values
	191	%
	192	% Usage:
	193	% md=collapse(md)
	194	%
	195	% See also: EXTRUDE, MODELEXTRACT
[13005]	196
[13692]	197	%Check that the model is really a 3d model
[17687]	198	if ~strcmp(md.mesh.elementtype(),'Penta'),
[13692]	199	error('collapse error message: only 3d mesh can be collapsed')
	200	end
[13005]	201
[17724]	202	%Start with changing all the fields from the 3d mesh
[13005]	203
[21827]	204	%dealing with the friction law
[13692]	205	%drag is limited to nodes that are on the bedrock.
[18775]	206	if isa(md.friction,'friction'),
	207	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	208	md.friction.p=project2d(md,md.friction.p,1);
	209	md.friction.q=project2d(md,md.friction.q,1);
[21819]	210	elseif isa(md.friction,'frictioncoulomb'),
	211	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	212	md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1);
	213	md.friction.p=project2d(md,md.friction.p,1);
	214	md.friction.q=project2d(md,md.friction.q,1);
[18775]	215	elseif isa(md.friction,'frictionhydro'),
	216	md.friction.q=project2d(md,md.friction.q,1);
	217	md.friction.C=project2d(md,md.friction.C,1);
	218	md.friction.As=project2d(md,md.friction.As,1);
[18798]	219	md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
[18775]	220	elseif isa(md.friction,'frictionwaterlayer'),
	221	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	222	md.friction.p=project2d(md,md.friction.p,1);
	223	md.friction.q=project2d(md,md.friction.q,1);
	224	md.friction.water_layer=project2d(md,md.friction.water_layer,1);
	225	elseif isa(md.friction,'frictionweertman'),
	226	md.friction.C=project2d(md,md.friction.C,1);
	227	md.friction.m=project2d(md,md.friction.m,1);
[19720]	228	elseif isa(md.friction,'frictionweertmantemp'),
	229	md.friction.C=project2d(md,md.friction.C,1);
	230	md.friction.m=project2d(md,md.friction.m,1);
	231	else
	232	disp('friction type not supported');
[21827]	233	end
[13005]	234
[13692]	235	%observations
	236	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
	237	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
	238	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
	239	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
	240	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
	241	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
[19527]	242	if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
	243	md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
	244	elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
	245	md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
[13692]	246	end;
[13005]	247
[13692]	248	%results
	249	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
	250	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
	251	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
	252	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
[18578]	253	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[18506]	254	if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
[18578]	255	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
	256	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
	257	if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
[21417]	258	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
	259	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
[21530]	260	%giaivins
[21584]	261	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
	262	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
[15021]	263
[13692]	264	%elementstype
	265	if ~isnan(md.flowequation.element_equation)
	266	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
	267	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]	268	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
	269	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
	270	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]	271	end
[13005]	272
[13692]	273	%boundary conditions
[15771]	274	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
	275	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
	276	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
	277	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
	278	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[15767]	279	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
[21544]	280	if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
[21417]	281	if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
[13692]	282	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]	283
[18506]	284	% Hydrologydc variables
	285	if isa(md.hydrology,'hydrologydc');
	286	md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
	287	md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
	288	md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
	289	md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
	290	if(md.hydrology.isefficientlayer==1)
	291	md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
[21808]	292	end
	293	end
[18506]	294
[13692]	295	%materials
	296	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
	297	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]	298
	299	%damage:
[17940]	300	if md.damage.isdamage,
	301	md.damage.D=DepthAverage(md,md.damage.D);
	302	end
[13005]	303
[13692]	304	%special for thermal modeling:
[18378]	305	if ~isnan(md.basalforcings.groundedice_melting_rate),
	306	md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
	307	end
[21417]	308	if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
[18378]	309	md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
	310	end
[13692]	311	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]	312
[21417]	313	if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
	314	md.calving.coeff=project2d(md,md.calving.coeff,1);
	315	end
[23652]	316	if isprop(md.frontalforcings,'meltingrate') & ~isnan(md.frontalforcings.meltingrate),
	317	md.frontalforcings.meltingrate=project2d(md,md.frontalforcings.meltingrate,1);
[21417]	318	end
	319
[13692]	320	%update of connectivity matrix
	321	md.mesh.average_vertex_connectivity=25;
[13005]	322
[13692]	323	%Collapse the mesh
	324	nodes2d=md.mesh.numberofvertices2d;
	325	elements2d=md.mesh.numberofelements2d;
[13005]	326
[13692]	327	%parameters
	328	md.geometry.surface=project2d(md,md.geometry.surface,1);
	329	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
[17590]	330	md.geometry.base=project2d(md,md.geometry.base,1);
[18480]	331	if ~isnan(md.geometry.bed),
	332	md.geometry.bed=project2d(md,md.geometry.bed,1);
	333	end
[17991]	334
[18378]	335	if ~isnan(md.mask.groundedice_levelset),
	336	md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
	337	end
	338	if ~isnan(md.mask.ice_levelset),
	339	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
	340	end
[13005]	341
[22955]	342	%lat long
	343	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
	344	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
	345
[21808]	346	%outputdefinitions
	347	for i=1:length(md.outputdefinition.definitions)
	348	if isobject(md.outputdefinition.definitions{i})
	349	%get subfields
	350	solutionsubfields=fields(md.outputdefinition.definitions{i});
	351	for j=1:length(solutionsubfields),
	352	field=md.outputdefinition.definitions{i}.(solutionsubfields{j});
	353	if length(field)==md.mesh.numberofvertices \| length(field)==md.mesh.numberofelements,
	354	md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1);
	355	end
	356	end
	357	end
	358	end
	359
[13692]	360	%Initialize with the 2d mesh
[17724]	361	mesh=mesh2d();
	362	mesh.x=md.mesh.x2d;
	363	mesh.y=md.mesh.y2d;
	364	mesh.numberofvertices=md.mesh.numberofvertices2d;
	365	mesh.numberofelements=md.mesh.numberofelements2d;
	366	mesh.elements=md.mesh.elements2d;
[21499]	367	if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end
	368	if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end
	369	mesh.epsg=md.mesh.epsg;
[22324]	370	if numel(md.mesh.scale_factor)==md.mesh.numberofvertices, mesh.scale_factor=project2d(md,md.mesh.scale_factor,1); end
[17991]	371	if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
	372	if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
[17724]	373	md.mesh=mesh;
[18738]	374	md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
	375	md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
[19955]	376	md.mesh.segments=contourenvelope(md.mesh);
[13005]	377
[13692]	378	end % }}}
[22955]	379	function md2 = extract(md,area,varargin) % {{{
[13692]	380	%extract - extract a model according to an Argus contour or flag list
	381	%
	382	% This routine extracts a submodel from a bigger model with respect to a given contour
	383	% md must be followed by the corresponding exp file or flags list
	384	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
	385	% If user wants every element outside the domain to be
[15564]	386	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]	387	% an empty string '' will be considered as an empty domain
	388	% a string 'all' will be considered as the entire domain
	389	%
	390	% Usage:
	391	% md2=extract(md,area);
	392	%
	393	% Examples:
	394	% md2=extract(md,'Domain.exp');
	395	%
	396	% See also: EXTRUDE, COLLAPSE
[13005]	397
[13692]	398	%copy model
	399	md1=md;
[13005]	400
[22955]	401	%recover optoins:
	402	options=pairoptions(varargin{:});
	403
[13692]	404	%some checks
[22955]	405	if ((nargin<2) \| (nargout~=1)),
[13692]	406	help extract
	407	error('extract error message: bad usage');
	408	end
[13005]	409
[13692]	410	%get elements that are inside area
	411	flag_elem=FlagElements(md1,area);
	412	if ~any(flag_elem),
	413	error('extracted model is empty');
	414	end
[13005]	415
[13692]	416	%kick out all elements with 3 dirichlets
[22955]	417	if getfieldvalue(options,'spccheck',1)
	418	spc_elem=find(~flag_elem);
	419	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
	420	flag=ones(md1.mesh.numberofvertices,1);
	421	flag(spc_node)=0;
	422	pos=find(sum(flag(md1.mesh.elements),2)==0);
	423	flag_elem(pos)=0;
	424	end
[13005]	425
[13692]	426	%extracted elements and nodes lists
	427	pos_elem=find(flag_elem);
	428	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]	429
[13692]	430	%keep track of some fields
	431	numberofvertices1=md1.mesh.numberofvertices;
	432	numberofelements1=md1.mesh.numberofelements;
	433	numberofvertices2=length(pos_node);
	434	numberofelements2=length(pos_elem);
	435	flag_node=zeros(numberofvertices1,1);
	436	flag_node(pos_node)=1;
[13005]	437
[13692]	438	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
	439	Pelem=zeros(numberofelements1,1);
	440	Pelem(pos_elem)=[1:numberofelements2]';
	441	Pnode=zeros(numberofvertices1,1);
	442	Pnode(pos_node)=[1:numberofvertices2]';
[13005]	443
[13857]	444	%renumber the elements (some nodes won't exist anymore)
[13692]	445	elements_1=md1.mesh.elements;
	446	elements_2=elements_1(pos_elem,:);
	447	elements_2(:,1)=Pnode(elements_2(:,1));
	448	elements_2(:,2)=Pnode(elements_2(:,2));
	449	elements_2(:,3)=Pnode(elements_2(:,3));
[17558]	450	if isa(md1.mesh,'mesh3dprisms'),
[13692]	451	elements_2(:,4)=Pnode(elements_2(:,4));
	452	elements_2(:,5)=Pnode(elements_2(:,5));
	453	elements_2(:,6)=Pnode(elements_2(:,6));
	454	end
[13005]	455
[13857]	456	%OK, now create the new model!
[13005]	457
[13857]	458	%take every field from model
[13692]	459	md2=md1;
[13005]	460
[13692]	461	%automatically modify fields
[13005]	462
[13692]	463	%loop over model fields
	464	model_fields=fields(md1);
	465	for i=1:length(model_fields),
	466	%get field
	467	field=md1.(model_fields{i});
	468	fieldsize=size(field);
	469	if isobject(field), %recursive call
	470	object_fields=fields(md1.(model_fields{i}));
	471	for j=1:length(object_fields),
	472	%get field
	473	field=md1.(model_fields{i}).(object_fields{j});
	474	fieldsize=size(field);
	475	%size = number of nodes * n
	476	if fieldsize(1)==numberofvertices1
	477	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
	478	elseif (fieldsize(1)==numberofvertices1+1)
	479	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]	480	%size = number of elements * n
[13692]	481	elseif fieldsize(1)==numberofelements1
	482	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
[21428]	483	elseif (fieldsize(1)==numberofelements1+1)
	484	md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
[13692]	485	end
	486	end
	487	else
	488	%size = number of nodes * n
	489	if fieldsize(1)==numberofvertices1
	490	md2.(model_fields{i})=field(pos_node,:);
	491	elseif (fieldsize(1)==numberofvertices1+1)
	492	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]	493	%size = number of elements * n
[13692]	494	elseif fieldsize(1)==numberofelements1
	495	md2.(model_fields{i})=field(pos_elem,:);
[21428]	496	elseif (fieldsize(1)==numberofelements1+1)
	497	md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
[13692]	498	end
	499	end
	500	end
[13005]	501
[13692]	502	%modify some specific fields
[13005]	503
[13692]	504	%Mesh
	505	md2.mesh.numberofelements=numberofelements2;
	506	md2.mesh.numberofvertices=numberofvertices2;
	507	md2.mesh.elements=elements_2;
[13005]	508
[13692]	509	%mesh.uppervertex mesh.lowervertex
[17558]	510	if isa(md1.mesh,'mesh3dprisms'),
[13692]	511	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
	512	pos=find(~isnan(md2.mesh.uppervertex));
	513	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]	514
[13692]	515	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
	516	pos=find(~isnan(md2.mesh.lowervertex));
	517	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]	518
[13692]	519	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
	520	pos=find(~isnan(md2.mesh.upperelements));
	521	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]	522
[13692]	523	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
	524	pos=find(~isnan(md2.mesh.lowerelements));
	525	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
	526	end
[13005]	527
[13692]	528	%Initial 2d mesh
[17558]	529	if isa(md1.mesh,'mesh3dprisms'),
[13692]	530	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
	531	pos_elem_2d=find(flag_elem_2d);
	532	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
	533	pos_node_2d=find(flag_node_2d);
[13005]	534
[13692]	535	md2.mesh.numberofelements2d=length(pos_elem_2d);
	536	md2.mesh.numberofvertices2d=length(pos_node_2d);
	537	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
	538	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
	539	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
	540	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]	541
[13692]	542	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
	543	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
	544	end
[13005]	545
[13692]	546	%Edges
[17686]	547	if(dimension(md.mesh)==2),
[17563]	548	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
	549	%renumber first two columns
	550	pos=find(md2.mesh.edges(:,4)~=-1);
	551	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
	552	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
	553	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
	554	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
	555	%remove edges when the 2 vertices are not in the domain.
	556	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
	557	%Replace all zeros by -1 in the last two columns
	558	pos=find(md2.mesh.edges(:,3)==0);
	559	md2.mesh.edges(pos,3)=-1;
	560	pos=find(md2.mesh.edges(:,4)==0);
	561	md2.mesh.edges(pos,4)=-1;
	562	%Invert -1 on the third column with last column (Also invert first two columns!!)
	563	pos=find(md2.mesh.edges(:,3)==-1);
	564	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
	565	md2.mesh.edges(pos,4)=-1;
	566	values=md2.mesh.edges(pos,2);
	567	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
	568	md2.mesh.edges(pos,1)=values;
	569	%Finally remove edges that do not belong to any element
	570	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
	571	md2.mesh.edges(pos,:)=[];
	572	end
[13692]	573	end
[13005]	574
[13692]	575	%Penalties
[15771]	576	if ~isnan(md2.stressbalance.vertex_pairing),
	577	for i=1:size(md1.stressbalance.vertex_pairing,1);
	578	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]	579	end
[15771]	580	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]	581	end
[15767]	582	if ~isnan(md2.masstransport.vertex_pairing),
	583	for i=1:size(md1.masstransport.vertex_pairing,1);
	584	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]	585	end
[15767]	586	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]	587	end
[13005]	588
[13692]	589	%recreate segments
[20322]	590	if isa(md1.mesh,'mesh2d') \| isa(md1.mesh','mesh3dsurface'),
[13692]	591	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	592	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
[19957]	593	md2.mesh.segments=contourenvelope(md2.mesh);
[13692]	594	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
	595	else
	596	%First do the connectivity for the contourenvelope in 2d
	597	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
	598	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
[19957]	599	segments=contourenvelope(md2.mesh);
[17565]	600	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
[13692]	601	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
	602	%Then do it for 3d as usual
	603	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	604	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	605	end
[13005]	606
[13692]	607	%Boundary conditions: Dirichlets on new boundary
	608	%Catch the elements that have not been extracted
	609	orphans_elem=find(~flag_elem);
	610	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
	611	%Figure out which node are on the boundary between md2 and md1
	612	nodestoflag1=intersect(orphans_node,pos_node);
	613	nodestoflag2=Pnode(nodestoflag1);
[15771]	614	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
[13692]	615	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]	616	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
	617	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]	618	else
[15771]	619	md2.stressbalance.spcvx(nodestoflag2)=NaN;
	620	md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]	621	disp(' ')
	622	disp('!! extract warning: spc values should be checked !!')
	623	disp(' ')
	624	end
	625	%put 0 for vz
[15771]	626	md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]	627	end
	628	if ~isnan(md1.thermal.spctemperature),
	629	md2.thermal.spctemperature(nodestoflag2,1)=1;
	630	end
[13005]	631
[13692]	632	%Results fields
	633	if isstruct(md1.results),
	634	md2.results=struct();
	635	solutionfields=fields(md1.results);
	636	for i=1:length(solutionfields),
[14230]	637	if isstruct(md1.results.(solutionfields{i}))
	638	%get subfields
	639	solutionsubfields=fields(md1.results.(solutionfields{i}));
	640	for j=1:length(solutionsubfields),
	641	field=md1.results.(solutionfields{i}).(solutionsubfields{j});
	642	if length(field)==numberofvertices1,
	643	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
	644	elseif length(field)==numberofelements1,
	645	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
	646	else
	647	md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
	648	end
	649	end
	650	else
	651	field=md1.results.(solutionfields{i});
[13692]	652	if length(field)==numberofvertices1,
[14230]	653	md2.results.(solutionfields{i})=field(pos_node);
[13692]	654	elseif length(field)==numberofelements1,
[14230]	655	md2.results.(solutionfields{i})=field(pos_elem);
[13692]	656	else
[14230]	657	md2.results.(solutionfields{i})=field;
[13692]	658	end
	659	end
	660	end
	661	end
[13005]	662
[21808]	663	%OutputDefinitions fields
	664	for i=1:length(md1.outputdefinition.definitions),
	665	if isobject(md1.outputdefinition.definitions{i})
	666	%get subfields
	667	solutionsubfields=fields(md1.outputdefinition.definitions{i});
	668	for j=1:length(solutionsubfields),
	669	field=md1.outputdefinition.definitions{i}.(solutionsubfields{j});
	670	if length(field)==numberofvertices1,
	671	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node);
	672	elseif length(field)==numberofelements1,
	673	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem);
	674	end
	675	end
	676	end
	677	end
	678
[13692]	679	%Keep track of pos_node and pos_elem
	680	md2.mesh.extractedvertices=pos_node;
	681	md2.mesh.extractedelements=pos_elem;
	682	end % }}}
	683	function md = extrude(md,varargin) % {{{
	684	%EXTRUDE - vertically extrude a 2d mesh
	685	%
	686	% vertically extrude a 2d mesh and create corresponding 3d mesh.
	687	% The vertical distribution can:
	688	% - follow a polynomial law
	689	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
	690	% - be discribed by a list of coefficients (between 0 and 1)
	691	%
	692	%
	693	% Usage:
	694	% md=extrude(md,numlayers,extrusionexponent);
	695	% md=extrude(md,numlayers,lowerexponent,upperexponent);
	696	% md=extrude(md,listofcoefficients);
	697	%
	698	% Example:
[18216]	699	% md=extrude(md,15,1.3);
	700	% md=extrude(md,15,1.3,1.2);
[13692]	701	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
	702	%
	703	% See also: MODELEXTRACT, COLLAPSE
[13005]	704
[13692]	705	%some checks on list of arguments
	706	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
	707	help extrude;
	708	error('extrude error message');
	709	end
[13005]	710
[13692]	711	%Extrude the mesh
	712	if nargin==2, %list of coefficients
	713	clist=varargin{1};
	714	if any(clist<0) \| any(clist>1),
	715	error('extrusioncoefficients must be between 0 and 1');
	716	end
	717	extrusionlist=sort(unique([clist(:);0;1]));
	718	numlayers=length(extrusionlist);
	719	elseif nargin==3, %one polynomial law
	720	if varargin{2}<=0,
	721	help extrude;
	722	error('extrusionexponent must be >=0');
	723	end
	724	numlayers=varargin{1};
	725	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
	726	elseif nargin==4, %two polynomial laws
	727	numlayers=varargin{1};
	728	lowerexp=varargin{2};
	729	upperexp=varargin{3};
[13005]	730
[13692]	731	if varargin{2}<=0 \| varargin{3}<=0,
	732	help extrude;
	733	error('lower and upper extrusionexponents must be >=0');
	734	end
[13005]	735
[13692]	736	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
	737	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
	738	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]	739
[13692]	740	end
[13005]	741
[13692]	742	if numlayers<2,
	743	error('number of layers should be at least 2');
	744	end
[17686]	745	if strcmp(md.mesh.domaintype(),'3D')
[13692]	746	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
	747	end
[13005]	748
[13692]	749	%Initialize with the 2d mesh
[17558]	750	mesh2d = md.mesh;
	751	md.mesh=mesh3dprisms();
	752	md.mesh.x = mesh2d.x;
	753	md.mesh.y = mesh2d.y;
	754	md.mesh.elements = mesh2d.elements;
	755	md.mesh.numberofelements = mesh2d.numberofelements;
	756	md.mesh.numberofvertices = mesh2d.numberofvertices;
	757
	758	md.mesh.lat = mesh2d.lat;
	759	md.mesh.long = mesh2d.long;
[18558]	760	md.mesh.epsg = mesh2d.epsg;
[22324]	761	md.mesh.scale_factor = mesh2d.scale_factor;
[17558]	762
	763	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
	764	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
	765	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
	766	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
	767
	768	md.mesh.extractedvertices = mesh2d.extractedvertices;
	769	md.mesh.extractedelements = mesh2d.extractedelements;
	770
[13692]	771	x3d=[];
	772	y3d=[];
	773	z3d=[]; %the lower node is on the bed
	774	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
[17590]	775	bed3d=md.geometry.base;
[13005]	776
[13692]	777	%Create the new layers
	778	for i=1:numlayers,
	779	x3d=[x3d; md.mesh.x];
	780	y3d=[y3d; md.mesh.y];
	781	%nodes are distributed between bed and surface accordingly to the given exponent
	782	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
	783	end
	784	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	785
[13692]	786	%Extrude elements
	787	elements3d=[];
	788	for i=1:numlayers-1,
	789	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
	790	end
	791	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	792
[13692]	793	%Keep a trace of lower and upper nodes
[17590]	794	lowervertex=NaN*ones(number_nodes3d,1);
	795	uppervertex=NaN*ones(number_nodes3d,1);
	796	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
	797	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
	798	md.mesh.lowervertex=lowervertex;
	799	md.mesh.uppervertex=uppervertex;
[13005]	800
[13692]	801	%same for lower and upper elements
[17590]	802	lowerelements=NaN*ones(number_el3d,1);
	803	upperelements=NaN*ones(number_el3d,1);
	804	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
	805	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
	806	md.mesh.lowerelements=lowerelements;
	807	md.mesh.upperelements=upperelements;
[13005]	808
[13692]	809	%Save old mesh
	810	md.mesh.x2d=md.mesh.x;
	811	md.mesh.y2d=md.mesh.y;
	812	md.mesh.elements2d=md.mesh.elements;
	813	md.mesh.numberofelements2d=md.mesh.numberofelements;
	814	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]	815
[13692]	816	%Build global 3d mesh
	817	md.mesh.elements=elements3d;
	818	md.mesh.x=x3d;
	819	md.mesh.y=y3d;
	820	md.mesh.z=z3d;
	821	md.mesh.numberofelements=number_el3d;
	822	md.mesh.numberofvertices=number_nodes3d;
	823	md.mesh.numberoflayers=numlayers;
[13005]	824
[13692]	825	%Ok, now deal with the other fields from the 2d mesh:
[13005]	826
[19048]	827	%bedinfo and surface info
	828	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
	829	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
	830	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
	831
[13692]	832	%lat long
	833	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
	834	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[22324]	835	md.mesh.scale_factor=project3d(md,'vector',md.mesh.scale_factor,'type','node');
[13005]	836
[19048]	837	md.geometry=extrude(md.geometry,md);
	838	md.friction = extrude(md.friction,md);
	839	md.inversion = extrude(md.inversion,md);
[19527]	840	md.smb = extrude(md.smb,md);
[19048]	841	md.initialization = extrude(md.initialization,md);
[13005]	842
[19050]	843	md.flowequation=md.flowequation.extrude(md);
[19048]	844	md.stressbalance=extrude(md.stressbalance,md);
[19050]	845	md.thermal=md.thermal.extrude(md);
	846	md.masstransport=md.masstransport.extrude(md);
[20460]	847	md.levelset=extrude(md.levelset,md);
[19048]	848	md.calving=extrude(md.calving,md);
[23652]	849	md.frontalforcings=extrude(md.frontalforcings,md);
[19048]	850	md.hydrology = extrude(md.hydrology,md);
[22955]	851	md.slr = extrude(md.slr,md);
[13005]	852
[13692]	853	%connectivity
[17991]	854	if ~isnan(md.mesh.elementconnectivity)
	855	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
	856	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
	857	for i=2:numlayers-1,
	858	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
	859	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
	860	end
	861	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13692]	862	end
[13005]	863
[19048]	864	md.materials=extrude(md.materials,md);
	865	md.damage=extrude(md.damage,md);
	866	md.mask=extrude(md.mask,md);
	867	md.qmu=extrude(md.qmu,md);
	868	md.basalforcings=extrude(md.basalforcings,md);
[21808]	869	md.outputdefinition=extrude(md.outputdefinition,md);
[13005]	870
[13692]	871	%increase connectivity if less than 25:
	872	if md.mesh.average_vertex_connectivity<=25,
	873	md.mesh.average_vertex_connectivity=100;
	874	end
[13005]	875	end % }}}
[13692]	876	function md = structtomodel(md,structmd) % {{{
[8952]	877
[13692]	878	if ~isstruct(structmd) error('input model is not a structure'); end
[8952]	879
[13692]	880	%loaded model is a struct, initialize output and recover all fields
	881	md = structtoobj(model,structmd);
[8952]	882
[13692]	883	%Old field now classes
	884	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
	885	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]	886
[13692]	887	%Field name change
	888	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	889	if isfield(structmd,'p'), md.friction.p=structmd.p; end
	890	if isfield(structmd,'q'), md.friction.q=structmd.p; end
[18378]	891	if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
[18068]	892	if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
[18378]	893	if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
[19527]	894	if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
[13692]	895	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
	896	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
	897	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
	898	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
[17610]	899	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
[13692]	900	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
	901	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
	902	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]	903	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]	904	if isfield(structmd,'g'), md.constants.g=structmd.g; end
	905	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
[19527]	906	if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
[18068]	907	if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
[13692]	908	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
	909	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	910	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
	911	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
	912	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
	913	if isfield(structmd,'riftproperties'), %old implementation
	914	md.rifts=rifts();
	915	md.rifts.riftproperties=structmd.riftproperties;
	916	md.rifts.riftstruct=structmd.rifts;
	917	md.rifts.riftproperties=structmd.riftinfo;
	918	end
	919	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
	920	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
	921	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
	922	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
	923	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
	924	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
	925	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
	926	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
	927	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
	928	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
	929	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
	930	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
	931	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
	932	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
	933	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
	934	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
	935	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
	936	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
	937	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
	938	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
	939	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
	940	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]	941	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
	942	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
	943	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
	944	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
	945	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]	946	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
	947	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
	948	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
	949	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]	950	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]	951	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
	952	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
	953	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]	954	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
	955	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]	956	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
	957	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
	958	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
	959	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]	960	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]	961	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]	962	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
	963	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
	964	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
	965	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
	966	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
	967	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
	968	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
	969	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
	970	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
	971	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
	972	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
	973	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
	974	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
	975	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
	976	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
	977	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
	978	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
	979	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
	980	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
	981	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
[17590]	982	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
[13692]	983	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
[17590]	984	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
[13692]	985	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
	986	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
	987	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
	988	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
	989	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
	990	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
	991	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
[22324]	992	if isfield(structmd,'scale_factor'), md.mesh.scale_factor=structmd.scale_factor; end
[13692]	993	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
	994	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
	995	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
	996	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
	997	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
	998	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
	999	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
	1000	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
	1001	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
	1002	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
	1003	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
	1004	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
	1005	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
	1006	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
	1007	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
	1008	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
[17610]	1009	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
[13692]	1010	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
	1011	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
	1012	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
	1013	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]	1014	if isfield(structmd,'edges'),
	1015	md.mesh.edges=structmd.edges;
	1016	md.mesh.edges(isnan(md.mesh.edges))=-1;
	1017	end
[13692]	1018	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
	1019	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
	1020	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
[15771]	1021	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]	1022	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
	1023	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]	1024
[13692]	1025	if isnumeric(md.verbose),
	1026	md.verbose=verbose;
	1027	end
[15768]	1028
[13692]	1029	if isfield(structmd,'spcvelocity'),
[15771]	1030	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1031	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1032	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1033	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
	1034	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
	1035	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]	1036	end
	1037	if isfield(structmd,'spcvx'),
[15771]	1038	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1039	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]	1040	end
	1041	if isfield(structmd,'spcvy'),
[15771]	1042	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1043	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]	1044	end
	1045	if isfield(structmd,'spcvz'),
[15771]	1046	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1047	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]	1048	end
[14620]	1049	if isfield(structmd,'pressureload'),
	1050	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]	1051	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
	1052	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
	1053	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]	1054	end
[13692]	1055	end
	1056	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
	1057	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
	1058	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
	1059	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
	1060	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
	1061	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
	1062	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
	1063	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
	1064	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
	1065	end
	1066	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
	1067	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
	1068	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
	1069	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
	1070	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
	1071	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
	1072	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
	1073	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
	1074	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
	1075	end
	1076	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
	1077	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
	1078	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
	1079	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
	1080	end
	1081	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
	1082	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
[17941]	1083	if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
[13692]	1084	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
	1085	end
	1086	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
	1087	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
	1088	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
	1089	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
	1090	end
	1091	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
	1092	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
	1093	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
	1094	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
	1095	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
	1096	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
	1097	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
	1098	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
	1099	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
	1100	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
	1101	end
[11659]	1102
[13692]	1103	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
	1104	md.thermal.stabilization=2;
[15767]	1105	md.masstransport.stabilization=1;
[13692]	1106	md.balancethickness.stabilization=1;
	1107	end
[15767]	1108	if isnumeric(md.masstransport.hydrostatic_adjustment)
	1109	if md.masstransport.hydrostatic_adjustment==269,
	1110	md.masstransport.hydrostatic_adjustment='Incremental';
[13692]	1111	else
[15767]	1112	md.masstransport.hydrostatic_adjustment='Absolute';
[13692]	1113	end
	1114	end
[8952]	1115
[13692]	1116	%New fields
[19124]	1117	if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1118	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
	1119	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
	1120	end
[19124]	1121	if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1122	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
	1123	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
	1124	end
	1125	if ~isfield(structmd,'diagnostic_ref');
[15771]	1126	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]	1127	end
[14529]	1128	if ~isfield(structmd,'loadingforce');
[15771]	1129	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]	1130	end
[15768]	1131
	1132	%2013 August 9
	1133	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
	1134	disp('Recovering old prognostic class');
	1135	md.masstransport=masstransport(structmd.prognostic);
	1136	end
[15771]	1137	%2013 August 9
[15775]	1138	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
[15771]	1139	disp('Recovering old diagnostic class');
[15775]	1140	md.stressbalance=stressbalance(structmd.diagnostic);
[15771]	1141	end
[19642]	1142	%2014 January 9th
[21148]	1143	if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
[19642]	1144	disp('Recovering old surfaceforcings class');
	1145	mass_balance=structmd.surfaceforcings.mass_balance;
	1146	md.smb=SMB();
	1147	md.smb.mass_balance=mass_balance;
	1148	end
	1149	%2015 September 10
[21148]	1150	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
[19642]	1151	disp('Recovering old SMB class');
	1152	md.smb=SMBforcing(structmd.surfaceforcings);
	1153	end
[21148]	1154	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
	1155	disp('Recovering old SMBhenning class');
	1156	md.smb=SMBhenning(structmd.surfaceforcings);
	1157	end
[13692]	1158	end% }}}
	1159	function md = setdefaultparameters(md) % {{{
[8926]	1160
[13692]	1161	%initialize subclasses
[17558]	1162	md.mesh = mesh2d();
[13692]	1163	md.mask = mask();
	1164	md.constants = constants();
	1165	md.geometry = geometry();
	1166	md.initialization = initialization();
[19527]	1167	md.smb = SMBforcing();
[13692]	1168	md.basalforcings = basalforcings();
	1169	md.friction = friction();
	1170	md.rifts = rifts();
[19984]	1171	md.slr = slr();
[13692]	1172	md.timestepping = timestepping();
	1173	md.groundingline = groundingline();
	1174	md.materials = matice();
[16160]	1175	md.damage = damage();
[13692]	1176	md.flowequation = flowequation();
	1177	md.debug = debug();
[14558]	1178	md.verbose = verbose();
[22296]	1179	md.settings = issmsettings();
[17932]	1180	md.toolkits = toolkits();
[13692]	1181	md.cluster = generic();
	1182	md.balancethickness = balancethickness();
[17079]	1183	md.stressbalance = stressbalance();
[14555]	1184	md.hydrology = hydrologyshreve();
[17079]	1185	md.masstransport = masstransport();
[13692]	1186	md.thermal = thermal();
	1187	md.steadystate = steadystate();
	1188	md.transient = transient();
[22040]	1189	md.levelset = levelset();
[18757]	1190	md.calving = calving();
[23652]	1191	md.frontalforcings = frontalforcings();
[22955]	1192	md.gia = giaivins();
	1193	md.esa = esa();
[22040]	1194	md.love = fourierlove();
[21260]	1195	md.esa = esa();
[13692]	1196	md.autodiff = autodiff();
	1197	md.inversion = inversion();
	1198	md.qmu = qmu();
[22955]	1199	md.amr = amr();
[13692]	1200	md.radaroverlay = radaroverlay();
	1201	md.results = struct();
[16388]	1202	md.outputdefinition = outputdefinition();
[13692]	1203	md.miscellaneous = miscellaneous();
	1204	md.private = private();
	1205	end
	1206	%}}}
[17483]	1207	function md = tetras(md,varargin) % {{{
	1208	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
	1209	%
	1210	% Usage:
	1211	% md=tetra(md)
	1212
	1213	if ~isa(md.mesh,'mesh3dprisms')
	1214	error('mesh is not a 3d prismatic mesh');
	1215	end
	1216
	1217	%Initialize tetra mesh
	1218	md.mesh=mesh3dtetras(md.mesh);
	1219
[17754]	1220	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
	1221	steiner = 0;
	1222	nbv = md.mesh.numberofvertices;
	1223	nbt = 3*md.mesh.numberofelements;
	1224	elements = zeros(nbt,4);
	1225	for i=1:md.mesh.numberofelements
	1226	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
	1227	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
	1228	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1229	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1230	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1231	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1232	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1233	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1234	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
	1235	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
	1236	elements(end+1,:) = [v2 v3 v5 v7];
	1237	elements(end+1,:) = [v3 v5 v6 v7];
	1238	elements(end+1,:) = [v1 v3 v6 v7];
	1239	elements(end+1,:) = [v1 v4 v6 v7];
	1240	elements(end+1,:) = [v4 v5 v6 v7];
	1241	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1242	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
	1243	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1244	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1245	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1246	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1247	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
	1248	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1249	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1250	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1251	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1252	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
[18142]	1253	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
[17754]	1254	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1255	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1256	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
	1257	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1258	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1259	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
	1260	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	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 v3 v4 v5];
	1263	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1264	elements(3*(i-1)+3,:) = [v3 v4 v5 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 v5 v6 v4];
	1267	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1268	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
	1269	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1270	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1271	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1272	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1273	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1274	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1275	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
	1276	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
	1277	elements(end+1,:) = [v2 v5 v6 v7];
	1278	elements(end+1,:) = [v2 v3 v6 v7];
	1279	elements(end+1,:) = [v3 v4 v6 v7];
	1280	elements(end+1,:) = [v1 v3 v4 v7];
	1281	elements(end+1,:) = [v4 v5 v6 v7];
	1282	else
	1283	error('Case not supported'); %not supposed to happen!
	1284	end
[17774]	1285	%Reorder elements to make sure they are direct
	1286	for j=1:3
	1287	element = elements(3*(i-1)+j,:);
	1288	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
	1289	if det(matrix)>0,
	1290	elements(3*(i-1)+j,1)=element(2);
	1291	elements(3*(i-1)+j,2)=element(1);
	1292	end
	1293	end
[17754]	1294	end
	1295	%%Split in 3 tetras
	1296	%subelement1 = [1 2 3 5];
	1297	%subelement2 = [4 6 5 1];
	1298	%subelement3 = [5 6 3 1];
	1299	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
[17774]	1300	if steiner==0,
	1301	disp('No Steiner point required to split prismatic mesh into tets');
	1302	else
	1303	disp([num2str(steiner) ' Steiner points had to be included'])
	1304	error('Steiner point not supported yet');
	1305	end
[17754]	1306
[17483]	1307	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
	1308
	1309	md.mesh.elements=elements;
	1310	md.mesh.numberofelements=size(elements,1);
	1311
	1312	%p and q (same deal, except for element that are on the bedrock: )
[17774]	1313	if ~isnan(md.friction.p),
	1314	md.friction.p=md.friction.p(pos_elements);
	1315	md.friction.q=md.friction.q(pos_elements);
	1316	end
[17483]	1317
	1318	%elementstype
	1319	if ~isnan(md.flowequation.element_equation)
	1320	oldelements_type=md.flowequation.element_equation;
	1321	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
	1322	end
	1323
	1324	%connectivity
	1325	md.mesh.elementconnectivity=NaN;
	1326
	1327	%materials
[17774]	1328	if ~isnan(md.materials.rheology_n),
	1329	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
	1330	end
[17483]	1331
	1332	%increase connectivity if less than 25:
	1333	if md.mesh.average_vertex_connectivity<=25,
	1334	md.mesh.average_vertex_connectivity=100;
	1335	end
	1336	end % }}}
[19040]	1337	function disp(self) % {{{
	1338	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
	1339	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
	1340	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
	1341	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
[19527]	1342	disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
[19040]	1343	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
	1344	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
	1345	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
	1346	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
	1347	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
	1348	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
	1349	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
	1350	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
[19984]	1351	disp(sprintf('%19s: %-22s -- %s','slr' ,['[1x1 ' class(self.slr) ']'],'slr forcings'));
[19040]	1352	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
	1353	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
	1354	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
	1355	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
	1356	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
	1357	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
	1358	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
	1359	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
	1360	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
	1361	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
	1362	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
	1363	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
	1364	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
[21544]	1365	disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
[19040]	1366	disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
[23652]	1367	disp(sprintf('%19s: %-22s -- %s','frontalforcings' ,['[1x1 ' class(self.frontalforcings) ']'],'parameters for frontalforcings'));
[22955]	1368	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
[21260]	1369	disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
[22955]	1370	disp(sprintf('%19s: %-22s -- %s','love' ,['[1x1 ' class(self.love) ']'],'parameters for love solution'));
[19040]	1371	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
	1372	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
	1373	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
[21674]	1374	disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
[19040]	1375	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
	1376	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
	1377	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
	1378	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
[13692]	1379	end % }}}
[19040]	1380	function memory(self) % {{{
[15106]	1381
[14611]	1382	disp(sprintf('\nMemory imprint:\n'));
[14307]	1383
[14603]	1384	fields=properties('model');
	1385	mem=0;
[15106]	1386
[14603]	1387	for i=1:length(fields),
[19040]	1388	field=self.(fields{i});
[14603]	1389	s=whos('field');
	1390	mem=mem+s.bytes/1e6;
[14611]	1391	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]	1392	end
[14603]	1393	disp(sprintf('%19s--%10s','--------------','--------------'));
	1394	disp(sprintf('%19s: %g Mb','Total',mem));
[14307]	1395	end % }}}
[19040]	1396	function netcdf(self,filename) % {{{
[14603]	1397	%NETCDF - save model as netcdf
	1398	%
	1399	% Usage:
	1400	% netcdf(md,filename)
	1401	%
	1402	% Example:
	1403	% netcdf(md,'model.nc');
	1404
	1405	disp('Saving model as NetCDF');
	1406	%1. Create NetCDF file
	1407	ncid=netcdf.create(filename,'CLOBBER');
	1408	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[19040]	1409	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
[14603]	1410	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
	1411	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
	1412
[14611]	1413	%Preallocate variable id, needed to write variables in netcdf file
[14631]	1414	var_id=zeros(1000,1);%preallocate
[14609]	1415
	1416	for step=1:2,
	1417	counter=0;
[19040]	1418	[var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
[14609]	1419	if step==1, netcdf.endDef(ncid); end
[14603]	1420	end
[14611]	1421
[14631]	1422	if counter>1000,
	1423	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]	1424	end
	1425
	1426	netcdf.close(ncid)
[14603]	1427	end % }}}
[19040]	1428	function xylim(self) % {{{
[14405]	1429
[19040]	1430	xlim([min(self.mesh.x) max(self.mesh.x)]);
	1431	ylim([min(self.mesh.y) max(self.mesh.y)])
[14405]	1432	end % }}}
[15316]	1433	function md=upload(md) % {{{
	1434	%the goal of this routine is to upload the model onto a server, and to empty it.
	1435	%So first, save the model with a unique name and upload the file to the server:
	1436	random_part=fix(rand(1)*10000);
	1437	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
	1438	eval(['save ' id ' md']);
	1439
	1440	%Now, upload the file:
	1441	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
	1442
	1443	%Now, empty this model of everything except settings, and record name of file we just uploaded!
	1444	settings_back=md.settings;
	1445	md=model();
	1446	md.settings=settings_back;
	1447	md.settings.upload_filename=id;
	1448
	1449	%get locally rid of file that was uploaded
	1450	eval(['delete ' id]);
	1451
	1452	end % }}}
	1453	function md=download(md) % {{{
[15643]	1454
[15316]	1455	%the goal of this routine is to download the internals of the current model from a server, because
	1456	%this model is empty, except for the settings which tell us where to go and find this model!
[15643]	1457
[15316]	1458	%Download the file:
	1459	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
	1460
	1461	name=md.settings.upload_filename;
	1462
	1463	%Now, load this model:
	1464	md=loadmodel(md.settings.upload_filename);
	1465
	1466	%get locally rid of file that was downloaded
	1467	eval(['delete ' name]);
	1468
	1469	end % }}}
[22955]	1470	function savemodeljs(md,modelname,websiteroot,varargin) % {{{
	1471
[19879]	1472	%the goal of this routine is to save the model as a javascript array that can be included in any html
	1473	%file:
	1474
[22955]	1475	options=pairoptions(varargin{:});
	1476	optimization=getfieldvalue(options,'optimize',0);
	1477
	1478
[19879]	1479	%disp:
[19894]	1480	disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
[19879]	1481
	1482	%open file for writing and declare the model:
[19894]	1483	fid=fopen([websiteroot '/js/' modelname '.js'],'w');
[19879]	1484	fprintf(fid,'var %s=new model();\n',modelname);
	1485
	1486	%now go through all the classes and fwrite all the corresponding fields:
	1487
	1488	fields=properties('model');
	1489	for i=1:length(fields),
	1490	field=fields{i};
	1491
	1492	%Some properties do not need to be saved
[19894]	1493	if ismember(field,{'results','cluster' }),
[19879]	1494	continue;
	1495	end
	1496
[22955]	1497	%some optimization:
	1498	if optimization==1,
	1499	%optimize for plotting only:
	1500	if ~ismember(field,{'geometry','mesh','mask'}),
	1501	continue;
	1502	end
	1503	end
	1504
[19879]	1505	%Check that current field is an object
	1506	if ~isobject(md.(field))
	1507	error(['field ''' char(field) ''' is not an object']);
	1508	end
	1509
	1510	%savemodeljs for current object
	1511	%disp(['javascript saving ' field '...']);
	1512	savemodeljs(md.(field),fid,modelname);
	1513	end
	1514
	1515	%done, close file:
	1516	fclose(fid);
	1517	end
[13692]	1518	end
[8926]	1519	end

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