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source: issm/trunk-jpl/src/m/classes/model.m@ 18578

Last change on this file since 18578 was 18578, checked in by bdef, 10 years ago
BUG:fixing colapsing of hydro
File size: 67.9 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;
	15	surfaceforcings = 0;
	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;
[9778]	24
[13692]	25	debug = 0;
	26	verbose = 0;
	27	settings = 0;
[14621]	28	toolkits = 0;
[13692]	29	cluster = 0;
[9778]	30
[13692]	31	balancethickness = 0;
[17757]	32	stressbalance = 0;
[13692]	33	groundingline = 0;
	34	hydrology = 0;
[17757]	35	masstransport = 0;
[13692]	36	thermal = 0;
	37	steadystate = 0;
	38	transient = 0;
[14724]	39	gia = 0;
[9778]	40
[18492]	41	seaice = 0;
	42
[13692]	43	autodiff = 0;
	44	flaim = 0;
	45	inversion = 0;
	46	qmu = 0;
[8926]	47
[13692]	48	results = 0;
[16388]	49	outputdefinition = 0;
[13692]	50	radaroverlay = 0;
	51	miscellaneous = 0;
	52	private = 0;
[9778]	53
[13692]	54	%}}}
	55	end
	56	methods (Static)
	57	function md = loadobj(md) % {{{
	58	% This function is directly called by matlab when a model object is
	59	% loaded. If the input is a struct it is an old version of model and
	60	% old fields must be recovered (make sure they are in the deprecated
	61	% model properties)
[8926]	62
[13692]	63	if verLessThan('matlab','7.9'),
	64	disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
	65	disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
[8952]	66
[13692]	67	% This is a Matlab bug: all the fields of md have their default value
	68	% Example of error message:
	69	% Warning: Error loading an object of class 'model':
	70	% Undefined function or method 'exist' for input arguments of type 'cell'
	71	%
	72	% This has been fixed in MATLAB 7.9 (R2009b) and later versions
	73	end
[8952]	74
[13692]	75	if isstruct(md)
	76	disp('Recovering model object from a previous version');
	77	md = structtomodel(model,md);
	78	end
[13239]	79
[13692]	80	%2012 August 4th
	81	if isa(md.materials,'materials'),
	82	disp('Recovering old materials');
	83	if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
[13718]	84	md.materials=matice(md.materials);
	85	else
[13692]	86	md.materials=matdamageice(md.materials);
	87	end
	88	end
[14559]	89	%2013 April 12
[15771]	90	if numel(md.stressbalance.loadingforce==1)
	91	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14559]	92	end
[14618]	93	%2013 April 17
	94	if isa(md.hydrology,'hydrology'),
	95	disp('Recovering old hydrology class');
	96	md.hydrology=hydrologyshreve(md.materials);
	97	end
[16356]	98	%2013 October 9
	99	if ~isa(md.damage,'damage'),
	100	md.damage=damage();
	101	md.damage.D=zeros(md.mesh.numberofvertices,1);
	102	md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
	103	end
[16822]	104	%2013 November 18
	105	if ~isa(md.outputdefinition,'outputdefinition'),
	106	md.outputdefinition=outputdefinition();
	107	end
[17079]	108	%2014 January 9th
	109	if isa(md.surfaceforcings,'surfaceforcings'),
	110	disp('Recovering old surfaceforcings class');
	111	mass_balance=md.surfaceforcings.mass_balance;
	112	md.surfaceforcings=SMB();
	113	md.surfaceforcings.mass_balance=mass_balance;
	114	end
[17558]	115	%2014 March 26th
	116	if isa(md.mesh,'mesh'),
[17566]	117	disp('Recovering old mesh class');
	118	if isprop(md.mesh,'dimension'),
	119	if md.mesh.dimension==2,
	120	md.mesh=mesh2d(md.mesh);
	121	else
	122	md.mesh=mesh3dprisms(md.mesh);
	123	end
[17558]	124	else
[17566]	125	md.mesh=mesh2dvertical(md.mesh);
[17558]	126	end
	127	end
[18506]	128	%2014 September 11
[18519]	129	if isa(md.seaice,'double');
[18538]	130	md.seaice=seaice();
[18519]	131	end
[13692]	132	end% }}}
	133	end
	134	methods
	135	function md = model(varargin) % {{{
[8926]	136
[13692]	137	switch nargin
	138	case 0
	139	md=setdefaultparameters(md);
[18492]	140	case 1
	141	if strcmpi(varargin{1},'seaice'),
	142	md=setdefaultparameters(md);
[18503]	143
	144	%Specific subject for sea ice model
	145	md.materials = matseaice();
[18492]	146	md.surfaceforcings = seaiceatm();
	147	md.basalforcings = seaiceocean();
	148	md.initialization = seaiceinitialization();
[18503]	149
	150	%Change some of the defauls
[18519]	151	md.timestepping.in_years = false;
	152	md.timestepping.time_step = 600;
	153	md.timestepping.final_time = 600;
	154	md.constants.g = 9.80616; %Same as TOPAZ
[18492]	155	else
	156	error('model constructor not supported yet');
	157	end
	158
[13692]	159	otherwise
	160	error('model constructor error message: 0 of 1 argument only in input.');
	161	end
	162	end
	163	%}}}
	164	function md = checkmessage(md,string) % {{{
	165	if(nargout~=1) error('wrong usage, model must be an output'); end
	166	disp(['model not consistent: ' string]);
	167	md.private.isconsistent=false;
	168	end
	169	%}}}
	170	function md = collapse(md)% {{{
	171	%COLLAPSE - collapses a 3d mesh into a 2d mesh
	172	%
	173	% This routine collapses a 3d model into a 2d model
	174	% and collapses all the fileds of the 3d model by
	175	% taking their depth-averaged values
	176	%
	177	% Usage:
	178	% md=collapse(md)
	179	%
	180	% See also: EXTRUDE, MODELEXTRACT
[13005]	181
[13692]	182	%Check that the model is really a 3d model
[17687]	183	if ~strcmp(md.mesh.elementtype(),'Penta'),
[13692]	184	error('collapse error message: only 3d mesh can be collapsed')
	185	end
[13005]	186
[17724]	187	%Start with changing all the fields from the 3d mesh
[13005]	188
[13692]	189	%drag is limited to nodes that are on the bedrock.
	190	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
[13005]	191
[13692]	192	%p and q (same deal, except for element that are on the bedrock: )
	193	md.friction.p=project2d(md,md.friction.p,1);
	194	md.friction.q=project2d(md,md.friction.q,1);
[13005]	195
[13692]	196	%observations
	197	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
	198	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
	199	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
	200	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
	201	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
	202	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
	203	if ~isnan(md.surfaceforcings.mass_balance),
	204	md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers);
	205	end;
	206	if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
[13005]	207
[13692]	208	%results
	209	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
	210	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
	211	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
	212	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
[18578]	213	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[18506]	214	if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
[18578]	215	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
	216	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
	217	if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
[15021]	218	%gia
	219	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
	220	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
	221
[13692]	222	%elementstype
	223	if ~isnan(md.flowequation.element_equation)
	224	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
	225	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]	226	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
	227	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
	228	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]	229	end
[13005]	230
[13692]	231	%boundary conditions
[15771]	232	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
	233	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
	234	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
	235	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
	236	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[15767]	237	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
[17991]	238	if ~isnan(md.damage.spcdamage), md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
[13692]	239	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]	240
[18506]	241	% Hydrologydc variables
	242	if isa(md.hydrology,'hydrologydc');
	243	md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
	244	md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
	245	md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
	246	md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
	247	if(md.hydrology.isefficientlayer==1)
	248	md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
	249	end
	250	end
	251
[13692]	252	%materials
	253	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
	254	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]	255
	256	%damage:
[17940]	257	if md.damage.isdamage,
	258	md.damage.D=DepthAverage(md,md.damage.D);
	259	end
[13005]	260
[13692]	261	%special for thermal modeling:
[18378]	262	if ~isnan(md.basalforcings.groundedice_melting_rate),
	263	md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
	264	end
	265	if ~isnan(md.basalforcings.floatingice_melting_rate),
	266	md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
	267	end
[13692]	268	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]	269
[13692]	270	%update of connectivity matrix
	271	md.mesh.average_vertex_connectivity=25;
[13005]	272
[13692]	273	%Collapse the mesh
	274	nodes2d=md.mesh.numberofvertices2d;
	275	elements2d=md.mesh.numberofelements2d;
[13005]	276
[13692]	277	%parameters
	278	md.geometry.surface=project2d(md,md.geometry.surface,1);
	279	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
[17590]	280	md.geometry.base=project2d(md,md.geometry.base,1);
[18480]	281	if ~isnan(md.geometry.bed),
	282	md.geometry.bed=project2d(md,md.geometry.bed,1);
	283	end
[17991]	284
[18378]	285	if ~isnan(md.mask.groundedice_levelset),
	286	md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
	287	end
	288	if ~isnan(md.mask.ice_levelset),
	289	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
	290	end
[13005]	291
[13692]	292	%lat long
	293	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
	294	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
[13005]	295
[13692]	296	%Initialize with the 2d mesh
[17724]	297	mesh=mesh2d();
	298	mesh.x=md.mesh.x2d;
	299	mesh.y=md.mesh.y2d;
	300	mesh.numberofvertices=md.mesh.numberofvertices2d;
	301	mesh.numberofelements=md.mesh.numberofelements2d;
	302	mesh.elements=md.mesh.elements2d;
[17991]	303	if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
	304	if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
[17724]	305	md.mesh=mesh;
[13005]	306
[13692]	307	end % }}}
	308	function md2 = extract(md,area) % {{{
	309	%extract - extract a model according to an Argus contour or flag list
	310	%
	311	% This routine extracts a submodel from a bigger model with respect to a given contour
	312	% md must be followed by the corresponding exp file or flags list
	313	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
	314	% If user wants every element outside the domain to be
[15564]	315	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]	316	% an empty string '' will be considered as an empty domain
	317	% a string 'all' will be considered as the entire domain
	318	%
	319	% Usage:
	320	% md2=extract(md,area);
	321	%
	322	% Examples:
	323	% md2=extract(md,'Domain.exp');
	324	%
	325	% See also: EXTRUDE, COLLAPSE
[13005]	326
[13692]	327	%copy model
	328	md1=md;
[13005]	329
[13692]	330	%some checks
	331	if ((nargin~=2) \| (nargout~=1)),
	332	help extract
	333	error('extract error message: bad usage');
	334	end
[13005]	335
[13692]	336	%get elements that are inside area
	337	flag_elem=FlagElements(md1,area);
	338	if ~any(flag_elem),
	339	error('extracted model is empty');
	340	end
[13005]	341
[13692]	342	%kick out all elements with 3 dirichlets
	343	spc_elem=find(~flag_elem);
	344	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
	345	flag=ones(md1.mesh.numberofvertices,1);
	346	flag(spc_node)=0;
	347	pos=find(sum(flag(md1.mesh.elements),2)==0);
	348	flag_elem(pos)=0;
[13005]	349
[13692]	350	%extracted elements and nodes lists
	351	pos_elem=find(flag_elem);
	352	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]	353
[13692]	354	%keep track of some fields
	355	numberofvertices1=md1.mesh.numberofvertices;
	356	numberofelements1=md1.mesh.numberofelements;
	357	numberofvertices2=length(pos_node);
	358	numberofelements2=length(pos_elem);
	359	flag_node=zeros(numberofvertices1,1);
	360	flag_node(pos_node)=1;
[13005]	361
[13692]	362	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
	363	Pelem=zeros(numberofelements1,1);
	364	Pelem(pos_elem)=[1:numberofelements2]';
	365	Pnode=zeros(numberofvertices1,1);
	366	Pnode(pos_node)=[1:numberofvertices2]';
[13005]	367
[13857]	368	%renumber the elements (some nodes won't exist anymore)
[13692]	369	elements_1=md1.mesh.elements;
	370	elements_2=elements_1(pos_elem,:);
	371	elements_2(:,1)=Pnode(elements_2(:,1));
	372	elements_2(:,2)=Pnode(elements_2(:,2));
	373	elements_2(:,3)=Pnode(elements_2(:,3));
[17558]	374	if isa(md1.mesh,'mesh3dprisms'),
[13692]	375	elements_2(:,4)=Pnode(elements_2(:,4));
	376	elements_2(:,5)=Pnode(elements_2(:,5));
	377	elements_2(:,6)=Pnode(elements_2(:,6));
	378	end
[13005]	379
[13857]	380	%OK, now create the new model!
[13005]	381
[13857]	382	%take every field from model
[13692]	383	md2=md1;
[13005]	384
[13692]	385	%automatically modify fields
[13005]	386
[13692]	387	%loop over model fields
	388	model_fields=fields(md1);
	389	for i=1:length(model_fields),
	390	%get field
	391	field=md1.(model_fields{i});
	392	fieldsize=size(field);
	393	if isobject(field), %recursive call
	394	object_fields=fields(md1.(model_fields{i}));
	395	for j=1:length(object_fields),
	396	%get field
	397	field=md1.(model_fields{i}).(object_fields{j});
	398	fieldsize=size(field);
	399	%size = number of nodes * n
	400	if fieldsize(1)==numberofvertices1
	401	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
	402	elseif (fieldsize(1)==numberofvertices1+1)
	403	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]	404	%size = number of elements * n
[13692]	405	elseif fieldsize(1)==numberofelements1
	406	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
	407	end
	408	end
	409	else
	410	%size = number of nodes * n
	411	if fieldsize(1)==numberofvertices1
	412	md2.(model_fields{i})=field(pos_node,:);
	413	elseif (fieldsize(1)==numberofvertices1+1)
	414	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]	415	%size = number of elements * n
[13692]	416	elseif fieldsize(1)==numberofelements1
	417	md2.(model_fields{i})=field(pos_elem,:);
	418	end
	419	end
	420	end
[13005]	421
[13692]	422	%modify some specific fields
[13005]	423
[13692]	424	%Mesh
	425	md2.mesh.numberofelements=numberofelements2;
	426	md2.mesh.numberofvertices=numberofvertices2;
	427	md2.mesh.elements=elements_2;
[13005]	428
[13692]	429	%mesh.uppervertex mesh.lowervertex
[17558]	430	if isa(md1.mesh,'mesh3dprisms'),
[13692]	431	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
	432	pos=find(~isnan(md2.mesh.uppervertex));
	433	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]	434
[13692]	435	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
	436	pos=find(~isnan(md2.mesh.lowervertex));
	437	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]	438
[13692]	439	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
	440	pos=find(~isnan(md2.mesh.upperelements));
	441	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]	442
[13692]	443	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
	444	pos=find(~isnan(md2.mesh.lowerelements));
	445	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
	446	end
[13005]	447
[13692]	448	%Initial 2d mesh
[17558]	449	if isa(md1.mesh,'mesh3dprisms'),
[13692]	450	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
	451	pos_elem_2d=find(flag_elem_2d);
	452	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
	453	pos_node_2d=find(flag_node_2d);
[13005]	454
[13692]	455	md2.mesh.numberofelements2d=length(pos_elem_2d);
	456	md2.mesh.numberofvertices2d=length(pos_node_2d);
	457	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
	458	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
	459	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
	460	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]	461
[13692]	462	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
	463	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
	464	end
[13005]	465
[13692]	466	%Edges
[17686]	467	if(dimension(md.mesh)==2),
[17563]	468	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
	469	%renumber first two columns
	470	pos=find(md2.mesh.edges(:,4)~=-1);
	471	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
	472	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
	473	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
	474	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
	475	%remove edges when the 2 vertices are not in the domain.
	476	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
	477	%Replace all zeros by -1 in the last two columns
	478	pos=find(md2.mesh.edges(:,3)==0);
	479	md2.mesh.edges(pos,3)=-1;
	480	pos=find(md2.mesh.edges(:,4)==0);
	481	md2.mesh.edges(pos,4)=-1;
	482	%Invert -1 on the third column with last column (Also invert first two columns!!)
	483	pos=find(md2.mesh.edges(:,3)==-1);
	484	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
	485	md2.mesh.edges(pos,4)=-1;
	486	values=md2.mesh.edges(pos,2);
	487	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
	488	md2.mesh.edges(pos,1)=values;
	489	%Finally remove edges that do not belong to any element
	490	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
	491	md2.mesh.edges(pos,:)=[];
	492	end
[13692]	493	end
[13005]	494
[13692]	495	%Penalties
[15771]	496	if ~isnan(md2.stressbalance.vertex_pairing),
	497	for i=1:size(md1.stressbalance.vertex_pairing,1);
	498	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]	499	end
[15771]	500	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]	501	end
[15767]	502	if ~isnan(md2.masstransport.vertex_pairing),
	503	for i=1:size(md1.masstransport.vertex_pairing,1);
	504	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]	505	end
[15767]	506	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]	507	end
[13005]	508
[13692]	509	%recreate segments
[17558]	510	if isa(md1.mesh,'mesh2d'),
[13692]	511	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	512	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	513	md2.mesh.segments=contourenvelope(md2);
	514	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
	515	else
	516	%First do the connectivity for the contourenvelope in 2d
	517	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
	518	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
[17565]	519	segments=contourenvelope(md2);
	520	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
[13692]	521	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
	522	%Then do it for 3d as usual
	523	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	524	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	525	end
[13005]	526
[13692]	527	%Boundary conditions: Dirichlets on new boundary
	528	%Catch the elements that have not been extracted
	529	orphans_elem=find(~flag_elem);
	530	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
	531	%Figure out which node are on the boundary between md2 and md1
	532	nodestoflag1=intersect(orphans_node,pos_node);
	533	nodestoflag2=Pnode(nodestoflag1);
[15771]	534	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
[13692]	535	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]	536	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
	537	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]	538	else
[15771]	539	md2.stressbalance.spcvx(nodestoflag2)=NaN;
	540	md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]	541	disp(' ')
	542	disp('!! extract warning: spc values should be checked !!')
	543	disp(' ')
	544	end
	545	%put 0 for vz
[15771]	546	md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]	547	end
	548	if ~isnan(md1.thermal.spctemperature),
	549	md2.thermal.spctemperature(nodestoflag2,1)=1;
	550	end
[13005]	551
[13692]	552	%Results fields
	553	if isstruct(md1.results),
	554	md2.results=struct();
	555	solutionfields=fields(md1.results);
	556	for i=1:length(solutionfields),
[14230]	557	if isstruct(md1.results.(solutionfields{i}))
	558	%get subfields
	559	solutionsubfields=fields(md1.results.(solutionfields{i}));
	560	for j=1:length(solutionsubfields),
	561	field=md1.results.(solutionfields{i}).(solutionsubfields{j});
	562	if length(field)==numberofvertices1,
	563	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
	564	elseif length(field)==numberofelements1,
	565	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
	566	else
	567	md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
	568	end
	569	end
	570	else
	571	field=md1.results.(solutionfields{i});
[13692]	572	if length(field)==numberofvertices1,
[14230]	573	md2.results.(solutionfields{i})=field(pos_node);
[13692]	574	elseif length(field)==numberofelements1,
[14230]	575	md2.results.(solutionfields{i})=field(pos_elem);
[13692]	576	else
[14230]	577	md2.results.(solutionfields{i})=field;
[13692]	578	end
	579	end
	580	end
	581	end
[13005]	582
[13692]	583	%Keep track of pos_node and pos_elem
	584	md2.mesh.extractedvertices=pos_node;
	585	md2.mesh.extractedelements=pos_elem;
	586	end % }}}
	587	function md = extrude(md,varargin) % {{{
	588	%EXTRUDE - vertically extrude a 2d mesh
	589	%
	590	% vertically extrude a 2d mesh and create corresponding 3d mesh.
	591	% The vertical distribution can:
	592	% - follow a polynomial law
	593	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
	594	% - be discribed by a list of coefficients (between 0 and 1)
	595	%
	596	%
	597	% Usage:
	598	% md=extrude(md,numlayers,extrusionexponent);
	599	% md=extrude(md,numlayers,lowerexponent,upperexponent);
	600	% md=extrude(md,listofcoefficients);
	601	%
	602	% Example:
[18216]	603	% md=extrude(md,15,1.3);
	604	% md=extrude(md,15,1.3,1.2);
[13692]	605	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
	606	%
	607	% See also: MODELEXTRACT, COLLAPSE
[13005]	608
[13692]	609	%some checks on list of arguments
	610	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
	611	help extrude;
	612	error('extrude error message');
	613	end
[13005]	614
[13692]	615	%Extrude the mesh
	616	if nargin==2, %list of coefficients
	617	clist=varargin{1};
	618	if any(clist<0) \| any(clist>1),
	619	error('extrusioncoefficients must be between 0 and 1');
	620	end
	621	extrusionlist=sort(unique([clist(:);0;1]));
	622	numlayers=length(extrusionlist);
	623	elseif nargin==3, %one polynomial law
	624	if varargin{2}<=0,
	625	help extrude;
	626	error('extrusionexponent must be >=0');
	627	end
	628	numlayers=varargin{1};
	629	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
	630	elseif nargin==4, %two polynomial laws
	631	numlayers=varargin{1};
	632	lowerexp=varargin{2};
	633	upperexp=varargin{3};
[13005]	634
[13692]	635	if varargin{2}<=0 \| varargin{3}<=0,
	636	help extrude;
	637	error('lower and upper extrusionexponents must be >=0');
	638	end
[13005]	639
[13692]	640	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
	641	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
	642	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]	643
[13692]	644	end
[13005]	645
[13692]	646	if numlayers<2,
	647	error('number of layers should be at least 2');
	648	end
[17686]	649	if strcmp(md.mesh.domaintype(),'3D')
[13692]	650	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
	651	end
[13005]	652
[13692]	653	%Initialize with the 2d mesh
[17558]	654	mesh2d = md.mesh;
	655	md.mesh=mesh3dprisms();
	656	md.mesh.x = mesh2d.x;
	657	md.mesh.y = mesh2d.y;
	658	md.mesh.elements = mesh2d.elements;
	659	md.mesh.numberofelements = mesh2d.numberofelements;
	660	md.mesh.numberofvertices = mesh2d.numberofvertices;
	661
	662	md.mesh.lat = mesh2d.lat;
	663	md.mesh.long = mesh2d.long;
[18558]	664	md.mesh.epsg = mesh2d.epsg;
[17558]	665
	666	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
	667	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
	668	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
	669	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
	670
	671	md.mesh.extractedvertices = mesh2d.extractedvertices;
	672	md.mesh.extractedelements = mesh2d.extractedelements;
	673
[13692]	674	x3d=[];
	675	y3d=[];
	676	z3d=[]; %the lower node is on the bed
	677	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
[17590]	678	bed3d=md.geometry.base;
[13005]	679
[13692]	680	%Create the new layers
	681	for i=1:numlayers,
	682	x3d=[x3d; md.mesh.x];
	683	y3d=[y3d; md.mesh.y];
	684	%nodes are distributed between bed and surface accordingly to the given exponent
	685	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
	686	end
	687	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	688
[13692]	689	%Extrude elements
	690	elements3d=[];
	691	for i=1:numlayers-1,
	692	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
	693	end
	694	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	695
[13692]	696	%Keep a trace of lower and upper nodes
[17590]	697	lowervertex=NaN*ones(number_nodes3d,1);
	698	uppervertex=NaN*ones(number_nodes3d,1);
	699	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
	700	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
	701	md.mesh.lowervertex=lowervertex;
	702	md.mesh.uppervertex=uppervertex;
[13005]	703
[13692]	704	%same for lower and upper elements
[17590]	705	lowerelements=NaN*ones(number_el3d,1);
	706	upperelements=NaN*ones(number_el3d,1);
	707	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
	708	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
	709	md.mesh.lowerelements=lowerelements;
	710	md.mesh.upperelements=upperelements;
[13005]	711
[13692]	712	%Save old mesh
	713	md.mesh.x2d=md.mesh.x;
	714	md.mesh.y2d=md.mesh.y;
	715	md.mesh.elements2d=md.mesh.elements;
	716	md.mesh.numberofelements2d=md.mesh.numberofelements;
	717	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]	718
[13692]	719	%Build global 3d mesh
	720	md.mesh.elements=elements3d;
	721	md.mesh.x=x3d;
	722	md.mesh.y=y3d;
	723	md.mesh.z=z3d;
	724	md.mesh.numberofelements=number_el3d;
	725	md.mesh.numberofvertices=number_nodes3d;
	726	md.mesh.numberoflayers=numlayers;
[13005]	727
[13692]	728	%Ok, now deal with the other fields from the 2d mesh:
[13005]	729
[13692]	730	%lat long
	731	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
	732	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[13005]	733
[13692]	734	%drag coefficient is limited to nodes that are on the bedrock.
	735	md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1);
[13005]	736
[13692]	737	%p and q (same deal, except for element that are on the bedrock: )
	738	md.friction.p=project3d(md,'vector',md.friction.p,'type','element');
	739	md.friction.q=project3d(md,'vector',md.friction.q,'type','element');
[13005]	740
[13692]	741	%observations
	742	md.inversion.vx_obs=project3d(md,'vector',md.inversion.vx_obs,'type','node');
	743	md.inversion.vy_obs=project3d(md,'vector',md.inversion.vy_obs,'type','node');
	744	md.inversion.vel_obs=project3d(md,'vector',md.inversion.vel_obs,'type','node');
[16577]	745	md.inversion.thickness_obs=project3d(md,'vector',md.inversion.thickness_obs,'type','node');
[17079]	746	md.surfaceforcings = extrude(md.surfaceforcings,md);
[13692]	747	md.balancethickness.thickening_rate=project3d(md,'vector',md.balancethickness.thickening_rate,'type','node');
[13005]	748
[13692]	749	%results
	750	if ~isnan(md.initialization.vx),md.initialization.vx=project3d(md,'vector',md.initialization.vx,'type','node');end;
	751	if ~isnan(md.initialization.vy),md.initialization.vy=project3d(md,'vector',md.initialization.vy,'type','node');end;
	752	if ~isnan(md.initialization.vz),md.initialization.vz=project3d(md,'vector',md.initialization.vz,'type','node');end;
	753	if ~isnan(md.initialization.vel),md.initialization.vel=project3d(md,'vector',md.initialization.vel,'type','node');end;
	754	if ~isnan(md.initialization.temperature),md.initialization.temperature=project3d(md,'vector',md.initialization.temperature,'type','node');end;
	755	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project3d(md,'vector',md.initialization.waterfraction,'type','node');end;
[16559]	756	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project3d(md,'vector',md.initialization.watercolumn,'type','node','layer',1);end;
	757	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project3d(md,'vector',md.initialization.sediment_head,'type','node','layer',1);end;
	758	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project3d(md,'vector',md.initialization.epl_head,'type','node','layer',1);end;
[17523]	759	if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project3d(md,'vector',md.initialization.epl_thickness,'type','node','layer',1);end;
[13005]	760
[13692]	761	%bedinfo and surface info
[17610]	762	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
[13692]	763	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
[13005]	764
[13692]	765	%elementstype
	766	if ~isnan(md.flowequation.element_equation)
	767	oldelements_type=md.flowequation.element_equation;
	768	md.flowequation.element_equation=zeros(number_el3d,1);
	769	md.flowequation.element_equation=project3d(md,'vector',oldelements_type,'type','element');
	770	end
[13005]	771
[13692]	772	%verticestype
	773	if ~isnan(md.flowequation.vertex_equation)
	774	oldvertices_type=md.flowequation.vertex_equation;
	775	md.flowequation.vertex_equation=zeros(number_nodes3d,1);
	776	md.flowequation.vertex_equation=project3d(md,'vector',oldvertices_type,'type','node');
	777	end
[15564]	778	md.flowequation.borderSSA=project3d(md,'vector',md.flowequation.borderSSA,'type','node');
	779	md.flowequation.borderHO=project3d(md,'vector',md.flowequation.borderHO,'type','node');
	780	md.flowequation.borderFS=project3d(md,'vector',md.flowequation.borderFS,'type','node');
[13005]	781
[13692]	782	%boundary conditions
[15771]	783	md.stressbalance.spcvx=project3d(md,'vector',md.stressbalance.spcvx,'type','node');
	784	md.stressbalance.spcvy=project3d(md,'vector',md.stressbalance.spcvy,'type','node');
	785	md.stressbalance.spcvz=project3d(md,'vector',md.stressbalance.spcvz,'type','node');
[13692]	786	md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',NaN);
[17562]	787	if (length(md.initialization.temperature)==md.mesh.numberofvertices),
	788	md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1);
	789	if isprop(md.mesh,'vertexonsurface'),
	790	pos=find(md.mesh.vertexonsurface);
	791	md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface
	792	end
	793	end
[15767]	794	md.masstransport.spcthickness=project3d(md,'vector',md.masstransport.spcthickness,'type','node');
[17435]	795	md.masstransport.calvingrate=project3d(md,'vector',md.masstransport.calvingrate,'type','node');
[13692]	796	md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
[16190]	797	md.damage.spcdamage=project3d(md,'vector',md.damage.spcdamage,'type','node');
[15771]	798	md.stressbalance.referential=project3d(md,'vector',md.stressbalance.referential,'type','node');
	799	md.stressbalance.loadingforce=project3d(md,'vector',md.stressbalance.loadingforce,'type','node');
[17422]	800
	801	% Hydrologydc variables
[16559]	802	if isa(md.hydrology,'hydrologydc');
	803	md.hydrology.spcsediment_head=project3d(md,'vector',md.hydrology.spcsediment_head,'type','node','layer',1);
[16861]	804	md.hydrology.mask_eplactive_node=project3d(md,'vector',md.hydrology.mask_eplactive_node,'type','node','layer',1);
[17022]	805	md.hydrology.sediment_transmitivity=project3d(md,'vector',md.hydrology.sediment_transmitivity,'type','node','layer',1);
[17422]	806	md.hydrology.basal_moulin_input=project3d(md,'vector',md.hydrology.basal_moulin_input,'type','node','layer',1);
[18506]	807	if(md.hydrology.isefficientlayer==1);
	808	md.hydrology.spcepl_head=project3d(md,'vector',md.hydrology.spcepl_head,'type','node','layer',1);
	809	end
[16559]	810	end
[13005]	811
[13692]	812	%connectivity
[17991]	813	if ~isnan(md.mesh.elementconnectivity)
	814	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
	815	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
	816	for i=2:numlayers-1,
	817	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
	818	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
	819	end
	820	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13692]	821	end
[13005]	822
[13692]	823	%materials
	824	md.materials.rheology_B=project3d(md,'vector',md.materials.rheology_B,'type','node');
	825	md.materials.rheology_n=project3d(md,'vector',md.materials.rheology_n,'type','element');
[16160]	826
	827	%damage
	828	md.damage.D=project3d(md,'vector',md.damage.D,'type','node');
[13005]	829
[13692]	830	%parameters
	831	md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
	832	md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
[14901]	833	md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node');
[14724]	834	md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node');
[13692]	835	md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
[17590]	836	md.geometry.base=project3d(md,'vector',md.geometry.base,'type','node');
[13692]	837	md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
	838	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
[15957]	839	md.mask.groundedice_levelset=project3d(md,'vector',md.mask.groundedice_levelset,'type','node');
[15943]	840	md.mask.ice_levelset=project3d(md,'vector',md.mask.ice_levelset,'type','node');
[13692]	841	if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end;
	842	if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end;
	843	if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end;
	844	if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end
[13005]	845
[13692]	846	%Put lithostatic pressure if there is an existing pressure
	847	if ~isnan(md.initialization.pressure),
	848	md.initialization.pressure=md.constants.gmd.materials.rho_ice(md.geometry.surface-md.mesh.z);
[18506]	849	end
[13005]	850
[13692]	851	%special for thermal modeling:
[18068]	852	md.basalforcings.groundedice_melting_rate=project3d(md,'vector',md.basalforcings.groundedice_melting_rate,'type','node','layer',1);
	853	md.basalforcings.floatingice_melting_rate=project3d(md,'vector',md.basalforcings.floatingice_melting_rate,'type','node','layer',1);
[13692]	854	if ~isnan(md.basalforcings.geothermalflux)
	855	md.basalforcings.geothermalflux=project3d(md,'vector',md.basalforcings.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux
	856	end
[13005]	857
[13692]	858	%increase connectivity if less than 25:
	859	if md.mesh.average_vertex_connectivity<=25,
	860	md.mesh.average_vertex_connectivity=100;
	861	end
[13005]	862	end % }}}
[13692]	863	function md = structtomodel(md,structmd) % {{{
[8952]	864
[13692]	865	if ~isstruct(structmd) error('input model is not a structure'); end
[8952]	866
[13692]	867	%loaded model is a struct, initialize output and recover all fields
	868	md = structtoobj(model,structmd);
[8952]	869
[13692]	870	%Old field now classes
	871	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
	872	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]	873
[13692]	874	%Field name change
	875	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	876	if isfield(structmd,'p'), md.friction.p=structmd.p; end
	877	if isfield(structmd,'q'), md.friction.q=structmd.p; end
[18378]	878	if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
[18068]	879	if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
[18378]	880	if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
[13692]	881	if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
	882	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
	883	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
	884	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
	885	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
[17610]	886	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
[13692]	887	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
	888	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
	889	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]	890	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]	891	if isfield(structmd,'g'), md.constants.g=structmd.g; end
	892	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
	893	if isfield(structmd,'surface_mass_balance'), md.surfaceforcings.mass_balance=structmd.surface_mass_balance; end
[18068]	894	if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
[13692]	895	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
	896	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	897	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
	898	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
	899	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
	900	if isfield(structmd,'riftproperties'), %old implementation
	901	md.rifts=rifts();
	902	md.rifts.riftproperties=structmd.riftproperties;
	903	md.rifts.riftstruct=structmd.rifts;
	904	md.rifts.riftproperties=structmd.riftinfo;
	905	end
	906	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
	907	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
	908	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
	909	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
	910	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
	911	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
	912	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
	913	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
	914	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
	915	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
	916	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
	917	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
	918	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
	919	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
	920	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
	921	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
	922	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
	923	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
	924	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
	925	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
	926	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
	927	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]	928	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
	929	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
	930	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
	931	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
	932	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]	933	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
	934	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
	935	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
	936	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]	937	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]	938	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
	939	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
	940	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]	941	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
	942	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]	943	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
	944	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
	945	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
	946	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]	947	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]	948	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]	949	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
	950	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
	951	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
	952	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
	953	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
	954	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
	955	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
	956	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
	957	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
	958	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
	959	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
	960	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
	961	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
	962	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
	963	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
	964	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
	965	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
	966	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
	967	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
	968	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
[17590]	969	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
[13692]	970	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
[17590]	971	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
[13692]	972	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
	973	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
	974	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
	975	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
	976	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
	977	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
	978	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
	979	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
	980	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
	981	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
	982	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
	983	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
	984	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
	985	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
	986	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
	987	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
	988	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
	989	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
	990	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
	991	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
	992	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
	993	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
	994	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
[17610]	995	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
[13692]	996	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
	997	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
	998	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
	999	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]	1000	if isfield(structmd,'edges'),
	1001	md.mesh.edges=structmd.edges;
	1002	md.mesh.edges(isnan(md.mesh.edges))=-1;
	1003	end
[13692]	1004	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
	1005	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
	1006	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
	1007	if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
[15771]	1008	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]	1009	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
	1010	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]	1011
[13692]	1012	if isnumeric(md.verbose),
	1013	md.verbose=verbose;
	1014	end
[15768]	1015
[13692]	1016	if isfield(structmd,'spcvelocity'),
[15771]	1017	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1018	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1019	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1020	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
	1021	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
	1022	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]	1023	end
	1024	if isfield(structmd,'spcvx'),
[15771]	1025	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1026	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]	1027	end
	1028	if isfield(structmd,'spcvy'),
[15771]	1029	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1030	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]	1031	end
	1032	if isfield(structmd,'spcvz'),
[15771]	1033	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1034	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]	1035	end
[14620]	1036	if isfield(structmd,'pressureload'),
	1037	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]	1038	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
	1039	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
	1040	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]	1041	end
[13692]	1042	end
	1043	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
	1044	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
	1045	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
	1046	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
	1047	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
	1048	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
	1049	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
	1050	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
	1051	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
	1052	end
	1053	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
	1054	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
	1055	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
	1056	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
	1057	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
	1058	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
	1059	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
	1060	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
	1061	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
	1062	end
	1063	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
	1064	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
	1065	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
	1066	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
	1067	end
	1068	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
	1069	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
[17941]	1070	if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
[13692]	1071	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
	1072	end
	1073	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
	1074	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
	1075	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
	1076	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
	1077	end
	1078	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
	1079	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
	1080	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
	1081	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
	1082	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
	1083	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
	1084	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
	1085	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
	1086	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
	1087	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
	1088	end
[11659]	1089
[13692]	1090	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
	1091	md.thermal.stabilization=2;
[15767]	1092	md.masstransport.stabilization=1;
[13692]	1093	md.balancethickness.stabilization=1;
	1094	end
[15767]	1095	if isnumeric(md.masstransport.hydrostatic_adjustment)
	1096	if md.masstransport.hydrostatic_adjustment==269,
	1097	md.masstransport.hydrostatic_adjustment='Incremental';
[13692]	1098	else
[15767]	1099	md.masstransport.hydrostatic_adjustment='Absolute';
[13692]	1100	end
	1101	end
[8952]	1102
[13692]	1103	%New fields
	1104	if ~isfield(structmd,'upperelements');
	1105	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
	1106	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
	1107	end
	1108	if ~isfield(structmd,'lowerelements');
	1109	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
	1110	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
	1111	end
	1112	if ~isfield(structmd,'diagnostic_ref');
[15771]	1113	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]	1114	end
[14529]	1115	if ~isfield(structmd,'loadingforce');
[15771]	1116	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]	1117	end
[15768]	1118
	1119	%2013 August 9
	1120	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
	1121	disp('Recovering old prognostic class');
	1122	md.masstransport=masstransport(structmd.prognostic);
	1123	end
[15771]	1124	%2013 August 9
[15775]	1125	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
[15771]	1126	disp('Recovering old diagnostic class');
[15775]	1127	md.stressbalance=stressbalance(structmd.diagnostic);
[15771]	1128	end
[13692]	1129	end% }}}
	1130	function md = setdefaultparameters(md) % {{{
[8926]	1131
[13692]	1132	%initialize subclasses
[17558]	1133	md.mesh = mesh2d();
[13692]	1134	md.mask = mask();
	1135	md.constants = constants();
	1136	md.geometry = geometry();
	1137	md.initialization = initialization();
[17079]	1138	md.surfaceforcings = SMB();
[13692]	1139	md.basalforcings = basalforcings();
	1140	md.friction = friction();
	1141	md.rifts = rifts();
	1142	md.timestepping = timestepping();
	1143	md.groundingline = groundingline();
	1144	md.materials = matice();
[16160]	1145	md.damage = damage();
[13692]	1146	md.flowequation = flowequation();
	1147	md.debug = debug();
[14558]	1148	md.verbose = verbose();
[13692]	1149	md.settings = settings();
[17932]	1150	md.toolkits = toolkits();
[13692]	1151	md.cluster = generic();
	1152	md.balancethickness = balancethickness();
[17079]	1153	md.stressbalance = stressbalance();
[14555]	1154	md.hydrology = hydrologyshreve();
[17079]	1155	md.masstransport = masstransport();
[13692]	1156	md.thermal = thermal();
	1157	md.steadystate = steadystate();
	1158	md.transient = transient();
[14724]	1159	md.gia = gia();
[18492]	1160	md.seaice = seaice();
[13692]	1161	md.autodiff = autodiff();
	1162	md.flaim = flaim();
	1163	md.inversion = inversion();
	1164	md.qmu = qmu();
	1165	md.radaroverlay = radaroverlay();
	1166	md.results = struct();
[16388]	1167	md.outputdefinition = outputdefinition();
[13692]	1168	md.miscellaneous = miscellaneous();
	1169	md.private = private();
	1170	end
	1171	%}}}
[17483]	1172	function md = tetras(md,varargin) % {{{
	1173	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
	1174	%
	1175	% Usage:
	1176	% md=tetra(md)
	1177
	1178	if ~isa(md.mesh,'mesh3dprisms')
	1179	error('mesh is not a 3d prismatic mesh');
	1180	end
	1181
	1182	%Initialize tetra mesh
	1183	md.mesh=mesh3dtetras(md.mesh);
	1184
[17754]	1185	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
	1186	steiner = 0;
	1187	nbv = md.mesh.numberofvertices;
	1188	nbt = 3*md.mesh.numberofelements;
	1189	elements = zeros(nbt,4);
	1190	for i=1:md.mesh.numberofelements
	1191	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
	1192	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
	1193	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1194	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1195	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1196	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1197	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1198	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1199	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
	1200	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
	1201	elements(end+1,:) = [v2 v3 v5 v7];
	1202	elements(end+1,:) = [v3 v5 v6 v7];
	1203	elements(end+1,:) = [v1 v3 v6 v7];
	1204	elements(end+1,:) = [v1 v4 v6 v7];
	1205	elements(end+1,:) = [v4 v5 v6 v7];
	1206	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1207	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
	1208	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1209	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1210	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1211	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1212	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
	1213	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1214	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1215	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1216	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1217	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
[18142]	1218	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
[17754]	1219	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1220	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1221	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
	1222	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1223	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1224	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
	1225	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1226	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1227	elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
	1228	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1229	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1230	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1231	elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
	1232	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1233	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
	1234	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1235	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1236	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1237	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1238	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1239	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1240	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
	1241	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
	1242	elements(end+1,:) = [v2 v5 v6 v7];
	1243	elements(end+1,:) = [v2 v3 v6 v7];
	1244	elements(end+1,:) = [v3 v4 v6 v7];
	1245	elements(end+1,:) = [v1 v3 v4 v7];
	1246	elements(end+1,:) = [v4 v5 v6 v7];
	1247	else
	1248	error('Case not supported'); %not supposed to happen!
	1249	end
[17774]	1250	%Reorder elements to make sure they are direct
	1251	for j=1:3
	1252	element = elements(3*(i-1)+j,:);
	1253	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
	1254	if det(matrix)>0,
	1255	elements(3*(i-1)+j,1)=element(2);
	1256	elements(3*(i-1)+j,2)=element(1);
	1257	end
	1258	end
[17754]	1259	end
	1260	%%Split in 3 tetras
	1261	%subelement1 = [1 2 3 5];
	1262	%subelement2 = [4 6 5 1];
	1263	%subelement3 = [5 6 3 1];
	1264	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
[17774]	1265	if steiner==0,
	1266	disp('No Steiner point required to split prismatic mesh into tets');
	1267	else
	1268	disp([num2str(steiner) ' Steiner points had to be included'])
	1269	error('Steiner point not supported yet');
	1270	end
[17754]	1271
[17483]	1272	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
	1273
	1274	md.mesh.elements=elements;
	1275	md.mesh.numberofelements=size(elements,1);
	1276
	1277	%p and q (same deal, except for element that are on the bedrock: )
[17774]	1278	if ~isnan(md.friction.p),
	1279	md.friction.p=md.friction.p(pos_elements);
	1280	md.friction.q=md.friction.q(pos_elements);
	1281	end
[17483]	1282
	1283	%elementstype
	1284	if ~isnan(md.flowequation.element_equation)
	1285	oldelements_type=md.flowequation.element_equation;
	1286	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
	1287	end
	1288
	1289	%connectivity
	1290	md.mesh.elementconnectivity=NaN;
	1291
	1292	%materials
[17774]	1293	if ~isnan(md.materials.rheology_n),
	1294	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
	1295	end
[17483]	1296
	1297	%increase connectivity if less than 25:
	1298	if md.mesh.average_vertex_connectivity<=25,
	1299	md.mesh.average_vertex_connectivity=100;
	1300	end
	1301	end % }}}
[13692]	1302	function disp(obj) % {{{
	1303	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(obj.mesh) ']'],'mesh properties'));
	1304	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(obj.mask) ']'],'defines grounded and floating elements'));
	1305	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(obj.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
	1306	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(obj.constants) ']'],'physical constants'));
	1307	disp(sprintf('%19s: %-22s -- %s','surfaceforcings' ,['[1x1 ' class(obj.surfaceforcings) ']'],'surface forcings'));
	1308	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(obj.basalforcings) ']'],'bed forcings'));
	1309	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(obj.materials) ']'],'material properties'));
[17367]	1310	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(obj.damage) ']'],'parameters for damage evolution solution'));
[13692]	1311	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(obj.friction) ']'],'basal friction/drag properties'));
	1312	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(obj.flowequation) ']'],'flow equations'));
	1313	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(obj.timestepping) ']'],'time stepping for transient models'));
	1314	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(obj.initialization) ']'],'initial guess/state'));
	1315	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(obj.rifts) ']'],'rifts properties'));
	1316	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(obj.debug) ']'],'debugging tools (valgrind, gprof)'));
	1317	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
	1318	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
[14621]	1319	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(obj.toolkits) ']'],'PETSc options for each solution'));
[13692]	1320	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
	1321	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
[15771]	1322	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(obj.stressbalance) ']'],'parameters for stressbalance solution'));
[13692]	1323	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(obj.groundingline) ']'],'parameters for groundingline solution'));
	1324	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(obj.hydrology) ']'],'parameters for hydrology solution'));
[15767]	1325	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(obj.masstransport) ']'],'parameters for masstransport solution'));
[13692]	1326	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(obj.thermal) ']'],'parameters for thermal solution'));
	1327	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
	1328	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
[14724]	1329	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(obj.gia) ']'],'parameters for gia solution'));
[13692]	1330	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
	1331	disp(sprintf('%19s: %-22s -- %s','flaim' ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
	1332	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(obj.inversion) ']'],'parameters for inverse methods'));
	1333	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(obj.qmu) ']'],'dakota properties'));
[16388]	1334	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(obj.outputdefinition) ']'],'output definition'));
[13692]	1335	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(obj.results) ']'],'model results'));
	1336	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(obj.radaroverlay) ']'],'radar image for plot overlay'));
	1337	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields'));
[18492]	1338	disp(sprintf('%19s: %-22s -- %s','seaice' ,['[1x1 ' class(obj.seaice) ']'],'parameters for Sea Ice solution'));
[13692]	1339	end % }}}
[14307]	1340	function memory(obj) % {{{
[15106]	1341
[14611]	1342	disp(sprintf('\nMemory imprint:\n'));
[14307]	1343
[14603]	1344	fields=properties('model');
	1345	mem=0;
[15106]	1346
[14603]	1347	for i=1:length(fields),
	1348	field=obj.(fields{i});
	1349	s=whos('field');
	1350	mem=mem+s.bytes/1e6;
[14611]	1351	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]	1352	end
[14603]	1353	disp(sprintf('%19s--%10s','--------------','--------------'));
	1354	disp(sprintf('%19s: %g Mb','Total',mem));
[14307]	1355	end % }}}
[14603]	1356	function netcdf(obj,filename) % {{{
	1357	%NETCDF - save model as netcdf
	1358	%
	1359	% Usage:
	1360	% netcdf(md,filename)
	1361	%
	1362	% Example:
	1363	% netcdf(md,'model.nc');
	1364
	1365	disp('Saving model as NetCDF');
	1366	%1. Create NetCDF file
	1367	ncid=netcdf.create(filename,'CLOBBER');
	1368	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[14611]	1369	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' obj.miscellaneous.name ')']);
[14603]	1370	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
	1371	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
	1372
[14611]	1373	%Preallocate variable id, needed to write variables in netcdf file
[14631]	1374	var_id=zeros(1000,1);%preallocate
[14609]	1375
	1376	for step=1:2,
	1377	counter=0;
[14612]	1378	[var_id,counter]=structtonc(ncid,'md',obj,0,var_id,counter,step);
[14609]	1379	if step==1, netcdf.endDef(ncid); end
[14603]	1380	end
[14611]	1381
[14631]	1382	if counter>1000,
	1383	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]	1384	end
	1385
	1386	netcdf.close(ncid)
[14603]	1387	end % }}}
[14405]	1388	function xylim(obj) % {{{
	1389
	1390	xlim([min(obj.mesh.x) max(obj.mesh.x)]);
	1391	ylim([min(obj.mesh.y) max(obj.mesh.y)])
	1392	end % }}}
[15316]	1393	function md=upload(md) % {{{
	1394	%the goal of this routine is to upload the model onto a server, and to empty it.
	1395	%So first, save the model with a unique name and upload the file to the server:
	1396	random_part=fix(rand(1)*10000);
	1397	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
	1398	eval(['save ' id ' md']);
	1399
	1400	%Now, upload the file:
	1401	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
	1402
	1403	%Now, empty this model of everything except settings, and record name of file we just uploaded!
	1404	settings_back=md.settings;
	1405	md=model();
	1406	md.settings=settings_back;
	1407	md.settings.upload_filename=id;
	1408
	1409	%get locally rid of file that was uploaded
	1410	eval(['delete ' id]);
	1411
	1412	end % }}}
	1413	function md=download(md) % {{{
[15643]	1414
[15316]	1415	%the goal of this routine is to download the internals of the current model from a server, because
	1416	%this model is empty, except for the settings which tell us where to go and find this model!
[15643]	1417
[15316]	1418	%Download the file:
	1419	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
	1420
	1421	name=md.settings.upload_filename;
	1422
	1423	%Now, load this model:
	1424	md=loadmodel(md.settings.upload_filename);
	1425
	1426	%get locally rid of file that was downloaded
	1427	eval(['delete ' name]);
	1428
	1429	end % }}}
[13692]	1430	end
[8926]	1431	end

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