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source: issm/trunk-jpl/src/m/classes/model.m@ 17811

Last change on this file since 17811 was 17811, checked in by schlegel, 11 years ago
BUG: collapse accesses 2d mesh fields that no longer exist
File size: 65.8 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
[13692]	41	autodiff = 0;
	42	flaim = 0;
	43	inversion = 0;
	44	qmu = 0;
[8926]	45
[13692]	46	results = 0;
[16388]	47	outputdefinition = 0;
[13692]	48	radaroverlay = 0;
	49	miscellaneous = 0;
	50	private = 0;
[9778]	51
[13692]	52	%}}}
	53	end
	54	methods (Static)
	55	function md = loadobj(md) % {{{
	56	% This function is directly called by matlab when a model object is
	57	% loaded. If the input is a struct it is an old version of model and
	58	% old fields must be recovered (make sure they are in the deprecated
	59	% model properties)
[8926]	60
[13692]	61	if verLessThan('matlab','7.9'),
	62	disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
	63	disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
[8952]	64
[13692]	65	% This is a Matlab bug: all the fields of md have their default value
	66	% Example of error message:
	67	% Warning: Error loading an object of class 'model':
	68	% Undefined function or method 'exist' for input arguments of type 'cell'
	69	%
	70	% This has been fixed in MATLAB 7.9 (R2009b) and later versions
	71	end
[8952]	72
[13692]	73	if isstruct(md)
	74	disp('Recovering model object from a previous version');
	75	md = structtomodel(model,md);
	76	end
[13239]	77
[13692]	78	%2012 August 4th
	79	if isa(md.materials,'materials'),
	80	disp('Recovering old materials');
	81	if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
[13718]	82	md.materials=matice(md.materials);
	83	else
[13692]	84	md.materials=matdamageice(md.materials);
	85	end
	86	end
[14559]	87	%2013 April 12
[15771]	88	if numel(md.stressbalance.loadingforce==1)
	89	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14559]	90	end
[14618]	91	%2013 April 17
	92	if isa(md.hydrology,'hydrology'),
	93	disp('Recovering old hydrology class');
	94	md.hydrology=hydrologyshreve(md.materials);
	95	end
[16356]	96	%2013 October 9
	97	if ~isa(md.damage,'damage'),
	98	md.damage=damage();
	99	md.damage.D=zeros(md.mesh.numberofvertices,1);
	100	md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
	101	end
[16822]	102	%2013 November 18
	103	if ~isa(md.outputdefinition,'outputdefinition'),
	104	md.outputdefinition=outputdefinition();
	105	end
[17079]	106	%2014 January 9th
	107	if isa(md.surfaceforcings,'surfaceforcings'),
	108	disp('Recovering old surfaceforcings class');
	109	mass_balance=md.surfaceforcings.mass_balance;
	110	md.surfaceforcings=SMB();
	111	md.surfaceforcings.mass_balance=mass_balance;
	112	end
[17558]	113	%2014 March 26th
	114	if isa(md.mesh,'mesh'),
[17566]	115	disp('Recovering old mesh class');
	116	if isprop(md.mesh,'dimension'),
	117	if md.mesh.dimension==2,
	118	md.mesh=mesh2d(md.mesh);
	119	else
	120	md.mesh=mesh3dprisms(md.mesh);
	121	end
[17558]	122	else
[17566]	123	md.mesh=mesh2dvertical(md.mesh);
[17558]	124	end
	125	end
[13692]	126	end% }}}
	127	end
	128	methods
	129	function md = model(varargin) % {{{
[8926]	130
[13692]	131	switch nargin
	132	case 0
	133	md=setdefaultparameters(md);
	134	otherwise
	135	error('model constructor error message: 0 of 1 argument only in input.');
	136	end
	137	end
	138	%}}}
	139	function md = checkmessage(md,string) % {{{
	140	if(nargout~=1) error('wrong usage, model must be an output'); end
	141	disp(['model not consistent: ' string]);
	142	md.private.isconsistent=false;
	143	end
	144	%}}}
	145	function md = collapse(md)% {{{
	146	%COLLAPSE - collapses a 3d mesh into a 2d mesh
	147	%
	148	% This routine collapses a 3d model into a 2d model
	149	% and collapses all the fileds of the 3d model by
	150	% taking their depth-averaged values
	151	%
	152	% Usage:
	153	% md=collapse(md)
	154	%
	155	% See also: EXTRUDE, MODELEXTRACT
[13005]	156
[13692]	157	%Check that the model is really a 3d model
[17687]	158	if ~strcmp(md.mesh.elementtype(),'Penta'),
[13692]	159	error('collapse error message: only 3d mesh can be collapsed')
	160	end
[13005]	161
[17724]	162	%Start with changing all the fields from the 3d mesh
[13005]	163
[13692]	164	%drag is limited to nodes that are on the bedrock.
	165	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
[13005]	166
[13692]	167	%p and q (same deal, except for element that are on the bedrock: )
	168	md.friction.p=project2d(md,md.friction.p,1);
	169	md.friction.q=project2d(md,md.friction.q,1);
[13005]	170
[13692]	171	%observations
	172	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
	173	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
	174	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
	175	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
	176	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
	177	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
	178	if ~isnan(md.surfaceforcings.mass_balance),
	179	md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers);
	180	end;
	181	if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
[13005]	182
[13692]	183	%results
	184	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
	185	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
	186	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
	187	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
	188	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[13005]	189
[15021]	190	%gia
	191	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
	192	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
	193
[13692]	194	%elementstype
	195	if ~isnan(md.flowequation.element_equation)
	196	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
	197	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]	198	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
	199	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
	200	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]	201	end
[13005]	202
[13692]	203	%boundary conditions
[15771]	204	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
	205	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
	206	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
	207	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
	208	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[15767]	209	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
[16344]	210	md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers)
[13692]	211	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]	212
[13692]	213	%materials
	214	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
	215	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]	216
	217	%damage:
	218	md.damage.D=DepthAverage(md,md.damage.D);
[13005]	219
[13692]	220	%special for thermal modeling:
	221	md.basalforcings.melting_rate=project2d(md,md.basalforcings.melting_rate,1);
	222	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]	223
[13692]	224	%update of connectivity matrix
	225	md.mesh.average_vertex_connectivity=25;
[13005]	226
[13692]	227	%Collapse the mesh
	228	nodes2d=md.mesh.numberofvertices2d;
	229	elements2d=md.mesh.numberofelements2d;
[13005]	230
[13692]	231	%parameters
	232	md.geometry.surface=project2d(md,md.geometry.surface,1);
	233	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
[17590]	234	md.geometry.base=project2d(md,md.geometry.base,1);
[13692]	235	md.geometry.bed=project2d(md,md.geometry.bed,1);
	236	md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
	237	md.mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
[15943]	238	md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
	239	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
[13005]	240
[13692]	241	%lat long
	242	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
	243	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
[13005]	244
[13692]	245	%Initialize with the 2d mesh
[17724]	246	mesh=mesh2d();
	247	mesh.x=md.mesh.x2d;
	248	mesh.y=md.mesh.y2d;
	249	mesh.numberofvertices=md.mesh.numberofvertices2d;
	250	mesh.numberofelements=md.mesh.numberofelements2d;
	251	mesh.elements=md.mesh.elements2d;
	252	md.mesh=mesh;
[13005]	253
[13692]	254	end % }}}
	255	function md2 = extract(md,area) % {{{
	256	%extract - extract a model according to an Argus contour or flag list
	257	%
	258	% This routine extracts a submodel from a bigger model with respect to a given contour
	259	% md must be followed by the corresponding exp file or flags list
	260	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
	261	% If user wants every element outside the domain to be
[15564]	262	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]	263	% an empty string '' will be considered as an empty domain
	264	% a string 'all' will be considered as the entire domain
	265	%
	266	% Usage:
	267	% md2=extract(md,area);
	268	%
	269	% Examples:
	270	% md2=extract(md,'Domain.exp');
	271	%
	272	% See also: EXTRUDE, COLLAPSE
[13005]	273
[13692]	274	%copy model
	275	md1=md;
[13005]	276
[13692]	277	%some checks
	278	if ((nargin~=2) \| (nargout~=1)),
	279	help extract
	280	error('extract error message: bad usage');
	281	end
[13005]	282
[13692]	283	%get elements that are inside area
	284	flag_elem=FlagElements(md1,area);
	285	if ~any(flag_elem),
	286	error('extracted model is empty');
	287	end
[13005]	288
[13692]	289	%kick out all elements with 3 dirichlets
	290	spc_elem=find(~flag_elem);
	291	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
	292	flag=ones(md1.mesh.numberofvertices,1);
	293	flag(spc_node)=0;
	294	pos=find(sum(flag(md1.mesh.elements),2)==0);
	295	flag_elem(pos)=0;
[13005]	296
[13692]	297	%extracted elements and nodes lists
	298	pos_elem=find(flag_elem);
	299	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]	300
[13692]	301	%keep track of some fields
	302	numberofvertices1=md1.mesh.numberofvertices;
	303	numberofelements1=md1.mesh.numberofelements;
	304	numberofvertices2=length(pos_node);
	305	numberofelements2=length(pos_elem);
	306	flag_node=zeros(numberofvertices1,1);
	307	flag_node(pos_node)=1;
[13005]	308
[13692]	309	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
	310	Pelem=zeros(numberofelements1,1);
	311	Pelem(pos_elem)=[1:numberofelements2]';
	312	Pnode=zeros(numberofvertices1,1);
	313	Pnode(pos_node)=[1:numberofvertices2]';
[13005]	314
[13857]	315	%renumber the elements (some nodes won't exist anymore)
[13692]	316	elements_1=md1.mesh.elements;
	317	elements_2=elements_1(pos_elem,:);
	318	elements_2(:,1)=Pnode(elements_2(:,1));
	319	elements_2(:,2)=Pnode(elements_2(:,2));
	320	elements_2(:,3)=Pnode(elements_2(:,3));
[17558]	321	if isa(md1.mesh,'mesh3dprisms'),
[13692]	322	elements_2(:,4)=Pnode(elements_2(:,4));
	323	elements_2(:,5)=Pnode(elements_2(:,5));
	324	elements_2(:,6)=Pnode(elements_2(:,6));
	325	end
[13005]	326
[13857]	327	%OK, now create the new model!
[13005]	328
[13857]	329	%take every field from model
[13692]	330	md2=md1;
[13005]	331
[13692]	332	%automatically modify fields
[13005]	333
[13692]	334	%loop over model fields
	335	model_fields=fields(md1);
	336	for i=1:length(model_fields),
	337	%get field
	338	field=md1.(model_fields{i});
	339	fieldsize=size(field);
	340	if isobject(field), %recursive call
	341	object_fields=fields(md1.(model_fields{i}));
	342	for j=1:length(object_fields),
	343	%get field
	344	field=md1.(model_fields{i}).(object_fields{j});
	345	fieldsize=size(field);
	346	%size = number of nodes * n
	347	if fieldsize(1)==numberofvertices1
	348	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
	349	elseif (fieldsize(1)==numberofvertices1+1)
	350	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]	351	%size = number of elements * n
[13692]	352	elseif fieldsize(1)==numberofelements1
	353	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
	354	end
	355	end
	356	else
	357	%size = number of nodes * n
	358	if fieldsize(1)==numberofvertices1
	359	md2.(model_fields{i})=field(pos_node,:);
	360	elseif (fieldsize(1)==numberofvertices1+1)
	361	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]	362	%size = number of elements * n
[13692]	363	elseif fieldsize(1)==numberofelements1
	364	md2.(model_fields{i})=field(pos_elem,:);
	365	end
	366	end
	367	end
[13005]	368
[13692]	369	%modify some specific fields
[13005]	370
[13692]	371	%Mesh
	372	md2.mesh.numberofelements=numberofelements2;
	373	md2.mesh.numberofvertices=numberofvertices2;
	374	md2.mesh.elements=elements_2;
[13005]	375
[13692]	376	%mesh.uppervertex mesh.lowervertex
[17558]	377	if isa(md1.mesh,'mesh3dprisms'),
[13692]	378	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
	379	pos=find(~isnan(md2.mesh.uppervertex));
	380	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]	381
[13692]	382	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
	383	pos=find(~isnan(md2.mesh.lowervertex));
	384	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]	385
[13692]	386	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
	387	pos=find(~isnan(md2.mesh.upperelements));
	388	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]	389
[13692]	390	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
	391	pos=find(~isnan(md2.mesh.lowerelements));
	392	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
	393	end
[13005]	394
[13692]	395	%Initial 2d mesh
[17558]	396	if isa(md1.mesh,'mesh3dprisms'),
[13692]	397	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
	398	pos_elem_2d=find(flag_elem_2d);
	399	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
	400	pos_node_2d=find(flag_node_2d);
[13005]	401
[13692]	402	md2.mesh.numberofelements2d=length(pos_elem_2d);
	403	md2.mesh.numberofvertices2d=length(pos_node_2d);
	404	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
	405	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
	406	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
	407	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]	408
[13692]	409	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
	410	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
	411	end
[13005]	412
[13692]	413	%Edges
[17686]	414	if(dimension(md.mesh)==2),
[17563]	415	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
	416	%renumber first two columns
	417	pos=find(md2.mesh.edges(:,4)~=-1);
	418	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
	419	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
	420	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
	421	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
	422	%remove edges when the 2 vertices are not in the domain.
	423	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
	424	%Replace all zeros by -1 in the last two columns
	425	pos=find(md2.mesh.edges(:,3)==0);
	426	md2.mesh.edges(pos,3)=-1;
	427	pos=find(md2.mesh.edges(:,4)==0);
	428	md2.mesh.edges(pos,4)=-1;
	429	%Invert -1 on the third column with last column (Also invert first two columns!!)
	430	pos=find(md2.mesh.edges(:,3)==-1);
	431	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
	432	md2.mesh.edges(pos,4)=-1;
	433	values=md2.mesh.edges(pos,2);
	434	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
	435	md2.mesh.edges(pos,1)=values;
	436	%Finally remove edges that do not belong to any element
	437	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
	438	md2.mesh.edges(pos,:)=[];
	439	end
[13692]	440	end
[13005]	441
[13692]	442	%Penalties
[15771]	443	if ~isnan(md2.stressbalance.vertex_pairing),
	444	for i=1:size(md1.stressbalance.vertex_pairing,1);
	445	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]	446	end
[15771]	447	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]	448	end
[15767]	449	if ~isnan(md2.masstransport.vertex_pairing),
	450	for i=1:size(md1.masstransport.vertex_pairing,1);
	451	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]	452	end
[15767]	453	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]	454	end
[13005]	455
[13692]	456	%recreate segments
[17558]	457	if isa(md1.mesh,'mesh2d'),
[13692]	458	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	459	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	460	md2.mesh.segments=contourenvelope(md2);
	461	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
	462	else
	463	%First do the connectivity for the contourenvelope in 2d
	464	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
	465	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
[17565]	466	segments=contourenvelope(md2);
	467	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
[13692]	468	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
	469	%Then do it for 3d as usual
	470	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	471	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	472	end
[13005]	473
[13692]	474	%Boundary conditions: Dirichlets on new boundary
	475	%Catch the elements that have not been extracted
	476	orphans_elem=find(~flag_elem);
	477	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
	478	%Figure out which node are on the boundary between md2 and md1
	479	nodestoflag1=intersect(orphans_node,pos_node);
	480	nodestoflag2=Pnode(nodestoflag1);
[15771]	481	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
[13692]	482	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]	483	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
	484	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]	485	else
[15771]	486	md2.stressbalance.spcvx(nodestoflag2)=NaN;
	487	md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]	488	disp(' ')
	489	disp('!! extract warning: spc values should be checked !!')
	490	disp(' ')
	491	end
	492	%put 0 for vz
[15771]	493	md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]	494	end
	495	if ~isnan(md1.thermal.spctemperature),
	496	md2.thermal.spctemperature(nodestoflag2,1)=1;
	497	end
[13005]	498
[13692]	499	%Results fields
	500	if isstruct(md1.results),
	501	md2.results=struct();
	502	solutionfields=fields(md1.results);
	503	for i=1:length(solutionfields),
[14230]	504	if isstruct(md1.results.(solutionfields{i}))
	505	%get subfields
	506	solutionsubfields=fields(md1.results.(solutionfields{i}));
	507	for j=1:length(solutionsubfields),
	508	field=md1.results.(solutionfields{i}).(solutionsubfields{j});
	509	if length(field)==numberofvertices1,
	510	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
	511	elseif length(field)==numberofelements1,
	512	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
	513	else
	514	md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
	515	end
	516	end
	517	else
	518	field=md1.results.(solutionfields{i});
[13692]	519	if length(field)==numberofvertices1,
[14230]	520	md2.results.(solutionfields{i})=field(pos_node);
[13692]	521	elseif length(field)==numberofelements1,
[14230]	522	md2.results.(solutionfields{i})=field(pos_elem);
[13692]	523	else
[14230]	524	md2.results.(solutionfields{i})=field;
[13692]	525	end
	526	end
	527	end
	528	end
[13005]	529
[13692]	530	%Keep track of pos_node and pos_elem
	531	md2.mesh.extractedvertices=pos_node;
	532	md2.mesh.extractedelements=pos_elem;
	533	end % }}}
	534	function md = extrude(md,varargin) % {{{
	535	%EXTRUDE - vertically extrude a 2d mesh
	536	%
	537	% vertically extrude a 2d mesh and create corresponding 3d mesh.
	538	% The vertical distribution can:
	539	% - follow a polynomial law
	540	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
	541	% - be discribed by a list of coefficients (between 0 and 1)
	542	%
	543	%
	544	% Usage:
	545	% md=extrude(md,numlayers,extrusionexponent);
	546	% md=extrude(md,numlayers,lowerexponent,upperexponent);
	547	% md=extrude(md,listofcoefficients);
	548	%
	549	% Example:
	550	% md=extrude(md,8,3);
	551	% md=extrude(md,8,3,2);
	552	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
	553	%
	554	% See also: MODELEXTRACT, COLLAPSE
[13005]	555
[13692]	556	%some checks on list of arguments
	557	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
	558	help extrude;
	559	error('extrude error message');
	560	end
[13005]	561
[13692]	562	%Extrude the mesh
	563	if nargin==2, %list of coefficients
	564	clist=varargin{1};
	565	if any(clist<0) \| any(clist>1),
	566	error('extrusioncoefficients must be between 0 and 1');
	567	end
	568	extrusionlist=sort(unique([clist(:);0;1]));
	569	numlayers=length(extrusionlist);
	570	elseif nargin==3, %one polynomial law
	571	if varargin{2}<=0,
	572	help extrude;
	573	error('extrusionexponent must be >=0');
	574	end
	575	numlayers=varargin{1};
	576	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
	577	elseif nargin==4, %two polynomial laws
	578	numlayers=varargin{1};
	579	lowerexp=varargin{2};
	580	upperexp=varargin{3};
[13005]	581
[13692]	582	if varargin{2}<=0 \| varargin{3}<=0,
	583	help extrude;
	584	error('lower and upper extrusionexponents must be >=0');
	585	end
[13005]	586
[13692]	587	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
	588	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
	589	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]	590
[13692]	591	end
[13005]	592
[13692]	593	if numlayers<2,
	594	error('number of layers should be at least 2');
	595	end
[17686]	596	if strcmp(md.mesh.domaintype(),'3D')
[13692]	597	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
	598	end
[13005]	599
[13692]	600	%Initialize with the 2d mesh
[17558]	601	mesh2d = md.mesh;
	602	md.mesh=mesh3dprisms();
	603	md.mesh.x = mesh2d.x;
	604	md.mesh.y = mesh2d.y;
	605	md.mesh.elements = mesh2d.elements;
	606	md.mesh.numberofelements = mesh2d.numberofelements;
	607	md.mesh.numberofvertices = mesh2d.numberofvertices;
	608
	609	md.mesh.lat = mesh2d.lat;
	610	md.mesh.long = mesh2d.long;
	611	md.mesh.hemisphere = mesh2d.hemisphere;
	612
	613	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
	614	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
	615	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
	616	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
	617
	618	md.mesh.extractedvertices = mesh2d.extractedvertices;
	619	md.mesh.extractedelements = mesh2d.extractedelements;
	620
[13692]	621	x3d=[];
	622	y3d=[];
	623	z3d=[]; %the lower node is on the bed
	624	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
[17590]	625	bed3d=md.geometry.base;
[13005]	626
[13692]	627	%Create the new layers
	628	for i=1:numlayers,
	629	x3d=[x3d; md.mesh.x];
	630	y3d=[y3d; md.mesh.y];
	631	%nodes are distributed between bed and surface accordingly to the given exponent
	632	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
	633	end
	634	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	635
[13692]	636	%Extrude elements
	637	elements3d=[];
	638	for i=1:numlayers-1,
	639	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
	640	end
	641	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	642
[13692]	643	%Keep a trace of lower and upper nodes
[17590]	644	lowervertex=NaN*ones(number_nodes3d,1);
	645	uppervertex=NaN*ones(number_nodes3d,1);
	646	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
	647	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
	648	md.mesh.lowervertex=lowervertex;
	649	md.mesh.uppervertex=uppervertex;
[13005]	650
[13692]	651	%same for lower and upper elements
[17590]	652	lowerelements=NaN*ones(number_el3d,1);
	653	upperelements=NaN*ones(number_el3d,1);
	654	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
	655	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
	656	md.mesh.lowerelements=lowerelements;
	657	md.mesh.upperelements=upperelements;
[13005]	658
[13692]	659	%Save old mesh
	660	md.mesh.x2d=md.mesh.x;
	661	md.mesh.y2d=md.mesh.y;
	662	md.mesh.elements2d=md.mesh.elements;
	663	md.mesh.numberofelements2d=md.mesh.numberofelements;
	664	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]	665
[13692]	666	%Build global 3d mesh
	667	md.mesh.elements=elements3d;
	668	md.mesh.x=x3d;
	669	md.mesh.y=y3d;
	670	md.mesh.z=z3d;
	671	md.mesh.numberofelements=number_el3d;
	672	md.mesh.numberofvertices=number_nodes3d;
	673	md.mesh.numberoflayers=numlayers;
[13005]	674
[13692]	675	%Ok, now deal with the other fields from the 2d mesh:
[13005]	676
[13692]	677	%lat long
	678	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
	679	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[13005]	680
[13692]	681	%drag coefficient is limited to nodes that are on the bedrock.
	682	md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1);
[13005]	683
[13692]	684	%p and q (same deal, except for element that are on the bedrock: )
	685	md.friction.p=project3d(md,'vector',md.friction.p,'type','element');
	686	md.friction.q=project3d(md,'vector',md.friction.q,'type','element');
[13005]	687
[13692]	688	%observations
	689	md.inversion.vx_obs=project3d(md,'vector',md.inversion.vx_obs,'type','node');
	690	md.inversion.vy_obs=project3d(md,'vector',md.inversion.vy_obs,'type','node');
	691	md.inversion.vel_obs=project3d(md,'vector',md.inversion.vel_obs,'type','node');
[16577]	692	md.inversion.thickness_obs=project3d(md,'vector',md.inversion.thickness_obs,'type','node');
[17079]	693	md.surfaceforcings = extrude(md.surfaceforcings,md);
[13692]	694	md.balancethickness.thickening_rate=project3d(md,'vector',md.balancethickness.thickening_rate,'type','node');
[13005]	695
[13692]	696	%results
	697	if ~isnan(md.initialization.vx),md.initialization.vx=project3d(md,'vector',md.initialization.vx,'type','node');end;
	698	if ~isnan(md.initialization.vy),md.initialization.vy=project3d(md,'vector',md.initialization.vy,'type','node');end;
	699	if ~isnan(md.initialization.vz),md.initialization.vz=project3d(md,'vector',md.initialization.vz,'type','node');end;
	700	if ~isnan(md.initialization.vel),md.initialization.vel=project3d(md,'vector',md.initialization.vel,'type','node');end;
	701	if ~isnan(md.initialization.temperature),md.initialization.temperature=project3d(md,'vector',md.initialization.temperature,'type','node');end;
	702	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project3d(md,'vector',md.initialization.waterfraction,'type','node');end;
[16559]	703	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project3d(md,'vector',md.initialization.watercolumn,'type','node','layer',1);end;
	704	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project3d(md,'vector',md.initialization.sediment_head,'type','node','layer',1);end;
	705	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project3d(md,'vector',md.initialization.epl_head,'type','node','layer',1);end;
[17523]	706	if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project3d(md,'vector',md.initialization.epl_thickness,'type','node','layer',1);end;
[13005]	707
[13692]	708	%bedinfo and surface info
[17610]	709	md.mesh.elementonbase=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',1);
[13692]	710	md.mesh.elementonsurface=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',md.mesh.numberoflayers-1);
[17610]	711	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
[13692]	712	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
[13005]	713
[13692]	714	%elementstype
	715	if ~isnan(md.flowequation.element_equation)
	716	oldelements_type=md.flowequation.element_equation;
	717	md.flowequation.element_equation=zeros(number_el3d,1);
	718	md.flowequation.element_equation=project3d(md,'vector',oldelements_type,'type','element');
	719	end
[13005]	720
[13692]	721	%verticestype
	722	if ~isnan(md.flowequation.vertex_equation)
	723	oldvertices_type=md.flowequation.vertex_equation;
	724	md.flowequation.vertex_equation=zeros(number_nodes3d,1);
	725	md.flowequation.vertex_equation=project3d(md,'vector',oldvertices_type,'type','node');
	726	end
[15564]	727	md.flowequation.borderSSA=project3d(md,'vector',md.flowequation.borderSSA,'type','node');
	728	md.flowequation.borderHO=project3d(md,'vector',md.flowequation.borderHO,'type','node');
	729	md.flowequation.borderFS=project3d(md,'vector',md.flowequation.borderFS,'type','node');
[13005]	730
[13692]	731	%boundary conditions
[15771]	732	md.stressbalance.spcvx=project3d(md,'vector',md.stressbalance.spcvx,'type','node');
	733	md.stressbalance.spcvy=project3d(md,'vector',md.stressbalance.spcvy,'type','node');
	734	md.stressbalance.spcvz=project3d(md,'vector',md.stressbalance.spcvz,'type','node');
[13692]	735	md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',NaN);
[17562]	736	if (length(md.initialization.temperature)==md.mesh.numberofvertices),
	737	md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1);
	738	if isprop(md.mesh,'vertexonsurface'),
	739	pos=find(md.mesh.vertexonsurface);
	740	md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface
	741	end
	742	end
[15767]	743	md.masstransport.spcthickness=project3d(md,'vector',md.masstransport.spcthickness,'type','node');
[17435]	744	md.masstransport.calvingrate=project3d(md,'vector',md.masstransport.calvingrate,'type','node');
[13692]	745	md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
[16190]	746	md.damage.spcdamage=project3d(md,'vector',md.damage.spcdamage,'type','node');
[15771]	747	md.stressbalance.referential=project3d(md,'vector',md.stressbalance.referential,'type','node');
	748	md.stressbalance.loadingforce=project3d(md,'vector',md.stressbalance.loadingforce,'type','node');
[17422]	749
	750	% Hydrologydc variables
[16559]	751	if isa(md.hydrology,'hydrologydc');
	752	md.hydrology.spcsediment_head=project3d(md,'vector',md.hydrology.spcsediment_head,'type','node','layer',1);
	753	md.hydrology.spcepl_head=project3d(md,'vector',md.hydrology.spcepl_head,'type','node','layer',1);
[16861]	754	md.hydrology.mask_eplactive_node=project3d(md,'vector',md.hydrology.mask_eplactive_node,'type','node','layer',1);
[17022]	755	md.hydrology.sediment_transmitivity=project3d(md,'vector',md.hydrology.sediment_transmitivity,'type','node','layer',1);
[17422]	756	md.hydrology.basal_moulin_input=project3d(md,'vector',md.hydrology.basal_moulin_input,'type','node','layer',1);
[16559]	757	end
[13005]	758
[13692]	759	%connectivity
	760	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
	761	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
	762	for i=2:numlayers-1,
	763	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
	764	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
	765	end
	766	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13005]	767
[13692]	768	%materials
	769	md.materials.rheology_B=project3d(md,'vector',md.materials.rheology_B,'type','node');
	770	md.materials.rheology_n=project3d(md,'vector',md.materials.rheology_n,'type','element');
[16160]	771
	772	%damage
	773	md.damage.D=project3d(md,'vector',md.damage.D,'type','node');
[13005]	774
[13692]	775	%parameters
	776	md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
	777	md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
[14901]	778	md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node');
[14724]	779	md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node');
[13692]	780	md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
[17590]	781	md.geometry.base=project3d(md,'vector',md.geometry.base,'type','node');
[13692]	782	md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
	783	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
[15957]	784	md.mask.groundedice_levelset=project3d(md,'vector',md.mask.groundedice_levelset,'type','node');
[15943]	785	md.mask.ice_levelset=project3d(md,'vector',md.mask.ice_levelset,'type','node');
[13692]	786	if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end;
	787	if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end;
	788	if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end;
	789	if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end
[13005]	790
[13692]	791	%Put lithostatic pressure if there is an existing pressure
	792	if ~isnan(md.initialization.pressure),
	793	md.initialization.pressure=md.constants.gmd.materials.rho_ice(md.geometry.surface-md.mesh.z);
	794	end
[13005]	795
[13692]	796	%special for thermal modeling:
	797	md.basalforcings.melting_rate=project3d(md,'vector',md.basalforcings.melting_rate,'type','node','layer',1);
	798	if ~isnan(md.basalforcings.geothermalflux)
	799	md.basalforcings.geothermalflux=project3d(md,'vector',md.basalforcings.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux
	800	end
[13005]	801
[13692]	802	%increase connectivity if less than 25:
	803	if md.mesh.average_vertex_connectivity<=25,
	804	md.mesh.average_vertex_connectivity=100;
	805	end
[13005]	806	end % }}}
[13692]	807	function md = structtomodel(md,structmd) % {{{
[8952]	808
[13692]	809	if ~isstruct(structmd) error('input model is not a structure'); end
[8952]	810
[13692]	811	%loaded model is a struct, initialize output and recover all fields
	812	md = structtoobj(model,structmd);
[8952]	813
[13692]	814	%Old field now classes
	815	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
	816	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]	817
[13692]	818	%Field name change
	819	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	820	if isfield(structmd,'p'), md.friction.p=structmd.p; end
	821	if isfield(structmd,'q'), md.friction.q=structmd.p; end
	822	if isfield(structmd,'melting'), md.basalforcings.melting_rate=structmd.melting; end
	823	if isfield(structmd,'melting_rate'), md.basalforcings.melting_rate=structmd.melting_rate; end
	824	if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
	825	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
	826	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
	827	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
	828	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
[17610]	829	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
[13692]	830	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
	831	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
	832	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]	833	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]	834	if isfield(structmd,'g'), md.constants.g=structmd.g; end
	835	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
	836	if isfield(structmd,'surface_mass_balance'), md.surfaceforcings.mass_balance=structmd.surface_mass_balance; end
	837	if isfield(structmd,'basal_melting_rate'), md.basalforcings.melting_rate=structmd.basal_melting_rate; end
	838	if isfield(structmd,'basal_melting_rate_correction'), md.basalforcings.melting_rate_correction=structmd.basal_melting_rate_correction; end
	839	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
	840	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	841	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
	842	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
	843	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
	844	if isfield(structmd,'riftproperties'), %old implementation
	845	md.rifts=rifts();
	846	md.rifts.riftproperties=structmd.riftproperties;
	847	md.rifts.riftstruct=structmd.rifts;
	848	md.rifts.riftproperties=structmd.riftinfo;
	849	end
	850	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
	851	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
	852	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
	853	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
	854	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
	855	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
	856	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
	857	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
	858	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
	859	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
	860	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
	861	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
	862	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
	863	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
	864	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
	865	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
	866	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
	867	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
	868	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
	869	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
	870	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
	871	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]	872	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
	873	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
	874	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
	875	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
	876	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]	877	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
	878	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
	879	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
	880	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]	881	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]	882	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
	883	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
	884	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]	885	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
	886	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]	887	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
	888	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
	889	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
	890	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]	891	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]	892	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]	893	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
	894	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
	895	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
	896	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
	897	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
	898	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
	899	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
	900	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
	901	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
	902	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
	903	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
	904	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
	905	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
	906	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
	907	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
	908	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
	909	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
	910	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
	911	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
	912	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
[17590]	913	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
[13692]	914	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
[17590]	915	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
[13692]	916	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
	917	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
	918	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
	919	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
	920	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
	921	if isfield(structmd,'hemisphere'), md.mesh.hemisphere=structmd.hemisphere; end
	922	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
	923	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
	924	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
	925	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
	926	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
	927	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
	928	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
	929	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
	930	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
	931	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
	932	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
	933	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
	934	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
	935	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
	936	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
	937	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
	938	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
[17610]	939	if isfield(structmd,'elementonbase'), md.mesh.elementonbase=structmd.elementonbase; end
[13692]	940	if isfield(structmd,'elementonsurface'), md.mesh.elementonsurface=structmd.elementonsurface; end
	941	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
[17610]	942	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
[13692]	943	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
	944	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
	945	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
	946	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]	947	if isfield(structmd,'edges'),
	948	md.mesh.edges=structmd.edges;
	949	md.mesh.edges(isnan(md.mesh.edges))=-1;
	950	end
[13692]	951	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
	952	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
	953	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
	954	if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
[15771]	955	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]	956	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
	957	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]	958
[13692]	959	if isnumeric(md.verbose),
	960	md.verbose=verbose;
	961	end
[15768]	962
[13692]	963	if isfield(structmd,'spcvelocity'),
[15771]	964	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	965	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	966	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	967	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
	968	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
	969	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]	970	end
	971	if isfield(structmd,'spcvx'),
[15771]	972	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	973	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]	974	end
	975	if isfield(structmd,'spcvy'),
[15771]	976	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	977	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]	978	end
	979	if isfield(structmd,'spcvz'),
[15771]	980	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	981	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]	982	end
[14620]	983	if isfield(structmd,'pressureload'),
	984	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]	985	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
	986	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
	987	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]	988	end
[13692]	989	end
	990	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
	991	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
	992	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
	993	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
	994	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
	995	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
	996	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
	997	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
	998	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
	999	end
	1000	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
	1001	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
	1002	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
	1003	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
	1004	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
	1005	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
	1006	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
	1007	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
	1008	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
	1009	end
	1010	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
	1011	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
	1012	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
	1013	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
	1014	end
	1015	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
	1016	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
	1017	if (structmd.groundingline_migration==273), md.groundingline.migration='AgressiveMigration'; end
	1018	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
	1019	end
	1020	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
	1021	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
	1022	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
	1023	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
	1024	end
	1025	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
	1026	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
	1027	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
	1028	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
	1029	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
	1030	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
	1031	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
	1032	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
	1033	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
	1034	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
	1035	end
[11659]	1036
[13692]	1037	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
	1038	md.thermal.stabilization=2;
[15767]	1039	md.masstransport.stabilization=1;
[13692]	1040	md.balancethickness.stabilization=1;
	1041	end
[15767]	1042	if isnumeric(md.masstransport.hydrostatic_adjustment)
	1043	if md.masstransport.hydrostatic_adjustment==269,
	1044	md.masstransport.hydrostatic_adjustment='Incremental';
[13692]	1045	else
[15767]	1046	md.masstransport.hydrostatic_adjustment='Absolute';
[13692]	1047	end
	1048	end
[8952]	1049
[13692]	1050	%New fields
	1051	if ~isfield(structmd,'upperelements');
	1052	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
	1053	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
	1054	end
	1055	if ~isfield(structmd,'lowerelements');
	1056	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
	1057	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
	1058	end
	1059	if ~isfield(structmd,'diagnostic_ref');
[15771]	1060	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]	1061	end
[14529]	1062	if ~isfield(structmd,'loadingforce');
[15771]	1063	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]	1064	end
[15768]	1065
	1066	%2013 August 9
	1067	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
	1068	disp('Recovering old prognostic class');
	1069	md.masstransport=masstransport(structmd.prognostic);
	1070	end
[15771]	1071	%2013 August 9
[15775]	1072	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
[15771]	1073	disp('Recovering old diagnostic class');
[15775]	1074	md.stressbalance=stressbalance(structmd.diagnostic);
[15771]	1075	end
[13692]	1076	end% }}}
	1077	function md = setdefaultparameters(md) % {{{
[8926]	1078
[13692]	1079	%initialize subclasses
[17558]	1080	md.mesh = mesh2d();
[13692]	1081	md.mask = mask();
	1082	md.constants = constants();
	1083	md.geometry = geometry();
	1084	md.initialization = initialization();
[17079]	1085	md.surfaceforcings = SMB();
[13692]	1086	md.basalforcings = basalforcings();
	1087	md.friction = friction();
	1088	md.rifts = rifts();
	1089	md.timestepping = timestepping();
	1090	md.groundingline = groundingline();
	1091	md.materials = matice();
[16160]	1092	md.damage = damage();
[13692]	1093	md.flowequation = flowequation();
	1094	md.debug = debug();
[14558]	1095	md.verbose = verbose();
[13692]	1096	md.settings = settings();
[14621]	1097	md.toolkits = toolkits();
[13692]	1098	md.cluster = generic();
	1099	md.balancethickness = balancethickness();
[17079]	1100	md.stressbalance = stressbalance();
[14555]	1101	md.hydrology = hydrologyshreve();
[17079]	1102	md.masstransport = masstransport();
[13692]	1103	md.thermal = thermal();
	1104	md.steadystate = steadystate();
	1105	md.transient = transient();
[14724]	1106	md.gia = gia();
[13692]	1107	md.autodiff = autodiff();
	1108	md.flaim = flaim();
	1109	md.inversion = inversion();
	1110	md.qmu = qmu();
	1111	md.radaroverlay = radaroverlay();
	1112	md.results = struct();
[16388]	1113	md.outputdefinition = outputdefinition();
[13692]	1114	md.miscellaneous = miscellaneous();
	1115	md.private = private();
	1116	end
	1117	%}}}
[17483]	1118	function md = tetras(md,varargin) % {{{
	1119	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
	1120	%
	1121	% Usage:
	1122	% md=tetra(md)
	1123
	1124	if ~isa(md.mesh,'mesh3dprisms')
	1125	error('mesh is not a 3d prismatic mesh');
	1126	end
	1127
	1128	%Initialize tetra mesh
	1129	md.mesh=mesh3dtetras(md.mesh);
	1130
[17754]	1131	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
	1132	steiner = 0;
	1133	nbv = md.mesh.numberofvertices;
	1134	nbt = 3*md.mesh.numberofelements;
	1135	elements = zeros(nbt,4);
	1136	for i=1:md.mesh.numberofelements
	1137	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
	1138	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
	1139	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1140	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1141	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1142	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1143	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1144	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1145	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
	1146	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
	1147	elements(end+1,:) = [v2 v3 v5 v7];
	1148	elements(end+1,:) = [v3 v5 v6 v7];
	1149	elements(end+1,:) = [v1 v3 v6 v7];
	1150	elements(end+1,:) = [v1 v4 v6 v7];
	1151	elements(end+1,:) = [v4 v5 v6 v7];
	1152	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1153	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
	1154	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1155	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1156	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1157	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1158	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
	1159	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1160	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1161	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1162	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1163	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
	1164	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1165	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1166	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1167	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
	1168	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1169	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1170	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
	1171	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1172	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1173	elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
	1174	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1175	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1176	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1177	%NEW
	1178	elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
	1179	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1180	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
	1181	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1182	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1183	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1184	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1185	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1186	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1187	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
	1188	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
	1189	elements(end+1,:) = [v2 v5 v6 v7];
	1190	elements(end+1,:) = [v2 v3 v6 v7];
	1191	elements(end+1,:) = [v3 v4 v6 v7];
	1192	elements(end+1,:) = [v1 v3 v4 v7];
	1193	elements(end+1,:) = [v4 v5 v6 v7];
	1194	else
	1195	error('Case not supported'); %not supposed to happen!
	1196	end
[17774]	1197	%Reorder elements to make sure they are direct
	1198	for j=1:3
	1199	element = elements(3*(i-1)+j,:);
	1200	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
	1201	if det(matrix)>0,
	1202	elements(3*(i-1)+j,1)=element(2);
	1203	elements(3*(i-1)+j,2)=element(1);
	1204	end
	1205	end
[17754]	1206	end
	1207	%%Split in 3 tetras
	1208	%subelement1 = [1 2 3 5];
	1209	%subelement2 = [4 6 5 1];
	1210	%subelement3 = [5 6 3 1];
	1211	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
[17774]	1212	if steiner==0,
	1213	disp('No Steiner point required to split prismatic mesh into tets');
	1214	else
	1215	disp([num2str(steiner) ' Steiner points had to be included'])
	1216	error('Steiner point not supported yet');
	1217	end
[17754]	1218
[17483]	1219	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
	1220
	1221	md.mesh.elements=elements;
	1222	md.mesh.numberofelements=size(elements,1);
	1223
	1224	%p and q (same deal, except for element that are on the bedrock: )
[17774]	1225	if ~isnan(md.friction.p),
	1226	md.friction.p=md.friction.p(pos_elements);
	1227	md.friction.q=md.friction.q(pos_elements);
	1228	end
[17483]	1229
	1230	%elementstype
	1231	if ~isnan(md.flowequation.element_equation)
	1232	oldelements_type=md.flowequation.element_equation;
	1233	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
	1234	end
	1235
	1236	%connectivity
	1237	md.mesh.elementconnectivity=NaN;
	1238
	1239	%materials
[17774]	1240	if ~isnan(md.materials.rheology_n),
	1241	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
	1242	end
[17483]	1243
	1244	%increase connectivity if less than 25:
	1245	if md.mesh.average_vertex_connectivity<=25,
	1246	md.mesh.average_vertex_connectivity=100;
	1247	end
	1248	end % }}}
[13692]	1249	function disp(obj) % {{{
	1250	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(obj.mesh) ']'],'mesh properties'));
	1251	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(obj.mask) ']'],'defines grounded and floating elements'));
	1252	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(obj.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
	1253	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(obj.constants) ']'],'physical constants'));
	1254	disp(sprintf('%19s: %-22s -- %s','surfaceforcings' ,['[1x1 ' class(obj.surfaceforcings) ']'],'surface forcings'));
	1255	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(obj.basalforcings) ']'],'bed forcings'));
	1256	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(obj.materials) ']'],'material properties'));
[17367]	1257	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(obj.damage) ']'],'parameters for damage evolution solution'));
[13692]	1258	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(obj.friction) ']'],'basal friction/drag properties'));
	1259	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(obj.flowequation) ']'],'flow equations'));
	1260	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(obj.timestepping) ']'],'time stepping for transient models'));
	1261	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(obj.initialization) ']'],'initial guess/state'));
	1262	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(obj.rifts) ']'],'rifts properties'));
	1263	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(obj.debug) ']'],'debugging tools (valgrind, gprof)'));
	1264	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
	1265	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
[14621]	1266	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(obj.toolkits) ']'],'PETSc options for each solution'));
[13692]	1267	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
	1268	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
[15771]	1269	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(obj.stressbalance) ']'],'parameters for stressbalance solution'));
[13692]	1270	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(obj.groundingline) ']'],'parameters for groundingline solution'));
	1271	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(obj.hydrology) ']'],'parameters for hydrology solution'));
[15767]	1272	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(obj.masstransport) ']'],'parameters for masstransport solution'));
[13692]	1273	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(obj.thermal) ']'],'parameters for thermal solution'));
	1274	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
	1275	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
[14724]	1276	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(obj.gia) ']'],'parameters for gia solution'));
[13692]	1277	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
	1278	disp(sprintf('%19s: %-22s -- %s','flaim' ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
	1279	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(obj.inversion) ']'],'parameters for inverse methods'));
	1280	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(obj.qmu) ']'],'dakota properties'));
[16388]	1281	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(obj.outputdefinition) ']'],'output definition'));
[13692]	1282	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(obj.results) ']'],'model results'));
	1283	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(obj.radaroverlay) ']'],'radar image for plot overlay'));
	1284	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields'));
	1285	end % }}}
[14307]	1286	function memory(obj) % {{{
[15106]	1287
[14611]	1288	disp(sprintf('\nMemory imprint:\n'));
[14307]	1289
[14603]	1290	fields=properties('model');
	1291	mem=0;
[15106]	1292
[14603]	1293	for i=1:length(fields),
	1294	field=obj.(fields{i});
	1295	s=whos('field');
	1296	mem=mem+s.bytes/1e6;
[14611]	1297	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]	1298	end
[14603]	1299	disp(sprintf('%19s--%10s','--------------','--------------'));
	1300	disp(sprintf('%19s: %g Mb','Total',mem));
[14307]	1301	end % }}}
[14603]	1302	function netcdf(obj,filename) % {{{
	1303	%NETCDF - save model as netcdf
	1304	%
	1305	% Usage:
	1306	% netcdf(md,filename)
	1307	%
	1308	% Example:
	1309	% netcdf(md,'model.nc');
	1310
	1311	disp('Saving model as NetCDF');
	1312	%1. Create NetCDF file
	1313	ncid=netcdf.create(filename,'CLOBBER');
	1314	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[14611]	1315	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' obj.miscellaneous.name ')']);
[14603]	1316	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
	1317	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
	1318
[14611]	1319	%Preallocate variable id, needed to write variables in netcdf file
[14631]	1320	var_id=zeros(1000,1);%preallocate
[14609]	1321
	1322	for step=1:2,
	1323	counter=0;
[14612]	1324	[var_id,counter]=structtonc(ncid,'md',obj,0,var_id,counter,step);
[14609]	1325	if step==1, netcdf.endDef(ncid); end
[14603]	1326	end
[14611]	1327
[14631]	1328	if counter>1000,
	1329	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]	1330	end
	1331
	1332	netcdf.close(ncid)
[14603]	1333	end % }}}
[14405]	1334	function xylim(obj) % {{{
	1335
	1336	xlim([min(obj.mesh.x) max(obj.mesh.x)]);
	1337	ylim([min(obj.mesh.y) max(obj.mesh.y)])
	1338	end % }}}
[15316]	1339	function md=upload(md) % {{{
	1340	%the goal of this routine is to upload the model onto a server, and to empty it.
	1341	%So first, save the model with a unique name and upload the file to the server:
	1342	random_part=fix(rand(1)*10000);
	1343	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
	1344	eval(['save ' id ' md']);
	1345
	1346	%Now, upload the file:
	1347	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
	1348
	1349	%Now, empty this model of everything except settings, and record name of file we just uploaded!
	1350	settings_back=md.settings;
	1351	md=model();
	1352	md.settings=settings_back;
	1353	md.settings.upload_filename=id;
	1354
	1355	%get locally rid of file that was uploaded
	1356	eval(['delete ' id]);
	1357
	1358	end % }}}
	1359	function md=download(md) % {{{
[15643]	1360
[15316]	1361	%the goal of this routine is to download the internals of the current model from a server, because
	1362	%this model is empty, except for the settings which tell us where to go and find this model!
[15643]	1363
[15316]	1364	%Download the file:
	1365	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
	1366
	1367	name=md.settings.upload_filename;
	1368
	1369	%Now, load this model:
	1370	md=loadmodel(md.settings.upload_filename);
	1371
	1372	%get locally rid of file that was downloaded
	1373	eval(['delete ' name]);
	1374
	1375	end % }}}
[13692]	1376	end
[8926]	1377	end

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