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source: issm/trunk-jpl/src/m/classes/model.m@ 21544

Last change on this file since 21544 was 21544, checked in by Mathieu Morlighem, 8 years ago
BUG: keep old gia class
File size: 64.7 KB

Rev	Line
[8926]	1	%MODEL class definition
	2	%
	3	% Usage:
	4	% md = model(varargin)
	5
	6	classdef model
[13692]	7	properties (SetAccess=public) %Model fields
	8	% {{{
	9	%Careful here: no other class should be used as default value this is a bug of matlab
	10	mesh = 0;
	11	mask = 0;
[9778]	12
[13692]	13	geometry = 0;
	14	constants = 0;
[19527]	15	smb = 0;
[13692]	16	basalforcings = 0;
	17	materials = 0;
[16160]	18	damage = 0;
[13692]	19	friction = 0;
	20	flowequation = 0;
	21	timestepping = 0;
	22	initialization = 0;
	23	rifts = 0;
[19984]	24	slr = 0;
[9778]	25
[13692]	26	debug = 0;
	27	verbose = 0;
	28	settings = 0;
[14621]	29	toolkits = 0;
[13692]	30	cluster = 0;
[9778]	31
[13692]	32	balancethickness = 0;
[17757]	33	stressbalance = 0;
[13692]	34	groundingline = 0;
	35	hydrology = 0;
[17757]	36	masstransport = 0;
[13692]	37	thermal = 0;
	38	steadystate = 0;
	39	transient = 0;
[20460]	40	levelset = 0;
[18757]	41	calving = 0;
[21544]	42	giaivins = 0;
[21260]	43	esa = 0;
[9778]	44
[13692]	45	autodiff = 0;
	46	inversion = 0;
	47	qmu = 0;
[8926]	48
[13692]	49	results = 0;
[16388]	50	outputdefinition = 0;
[13692]	51	radaroverlay = 0;
	52	miscellaneous = 0;
	53	private = 0;
[9778]	54
[13692]	55	%}}}
	56	end
	57	methods (Static)
	58	function md = loadobj(md) % {{{
	59	% This function is directly called by matlab when a model object is
	60	% loaded. If the input is a struct it is an old version of model and
	61	% old fields must be recovered (make sure they are in the deprecated
	62	% model properties)
[8926]	63
[13692]	64	if verLessThan('matlab','7.9'),
	65	disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
	66	disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
[8952]	67
[13692]	68	% This is a Matlab bug: all the fields of md have their default value
	69	% Example of error message:
	70	% Warning: Error loading an object of class 'model':
	71	% Undefined function or method 'exist' for input arguments of type 'cell'
	72	%
	73	% This has been fixed in MATLAB 7.9 (R2009b) and later versions
	74	end
[8952]	75
[13692]	76	if isstruct(md)
	77	disp('Recovering model object from a previous version');
	78	md = structtomodel(model,md);
	79	end
[13239]	80
[13692]	81	%2012 August 4th
	82	if isa(md.materials,'materials'),
	83	disp('Recovering old materials');
	84	if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
[13718]	85	md.materials=matice(md.materials);
	86	else
[13692]	87	md.materials=matdamageice(md.materials);
	88	end
	89	end
[14559]	90	%2013 April 12
[15771]	91	if numel(md.stressbalance.loadingforce==1)
	92	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14559]	93	end
[14618]	94	%2013 April 17
	95	if isa(md.hydrology,'hydrology'),
	96	disp('Recovering old hydrology class');
	97	md.hydrology=hydrologyshreve(md.materials);
	98	end
[16356]	99	%2013 October 9
	100	if ~isa(md.damage,'damage'),
	101	md.damage=damage();
	102	md.damage.D=zeros(md.mesh.numberofvertices,1);
	103	md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
	104	end
[16822]	105	%2013 November 18
	106	if ~isa(md.outputdefinition,'outputdefinition'),
	107	md.outputdefinition=outputdefinition();
	108	end
[17558]	109	%2014 March 26th
	110	if isa(md.mesh,'mesh'),
[17566]	111	disp('Recovering old mesh class');
	112	if isprop(md.mesh,'dimension'),
	113	if md.mesh.dimension==2,
	114	md.mesh=mesh2d(md.mesh);
	115	else
	116	md.mesh=mesh3dprisms(md.mesh);
	117	end
[17558]	118	else
[17566]	119	md.mesh=mesh2dvertical(md.mesh);
[17558]	120	end
	121	end
[18775]	122	%2014 November 12
	123	if isa(md.calving,'double');
	124	md.calving=calving();
	125	end
[20059]	126	%2016 February 3
	127	if isa(md.slr,'double');
	128	md.slr=slr();
	129	end
[21260]	130	%2016 October 11
	131	if isa(md.esa,'double');
	132	md.esa=esa();
	133	end
[20460]	134
[13692]	135	end% }}}
	136	end
	137	methods
	138	function md = model(varargin) % {{{
[8926]	139
[13692]	140	switch nargin
	141	case 0
	142	md=setdefaultparameters(md);
[18492]	143	case 1
[19087]	144	error('model constructor not supported yet');
[18503]	145
[13692]	146	otherwise
	147	error('model constructor error message: 0 of 1 argument only in input.');
	148	end
	149	end
	150	%}}}
	151	function md = checkmessage(md,string) % {{{
	152	if(nargout~=1) error('wrong usage, model must be an output'); end
	153	disp(['model not consistent: ' string]);
	154	md.private.isconsistent=false;
	155	end
	156	%}}}
	157	function md = collapse(md)% {{{
	158	%COLLAPSE - collapses a 3d mesh into a 2d mesh
	159	%
	160	% This routine collapses a 3d model into a 2d model
	161	% and collapses all the fileds of the 3d model by
	162	% taking their depth-averaged values
	163	%
	164	% Usage:
	165	% md=collapse(md)
	166	%
	167	% See also: EXTRUDE, MODELEXTRACT
[13005]	168
[13692]	169	%Check that the model is really a 3d model
[17687]	170	if ~strcmp(md.mesh.elementtype(),'Penta'),
[13692]	171	error('collapse error message: only 3d mesh can be collapsed')
	172	end
[13005]	173
[17724]	174	%Start with changing all the fields from the 3d mesh
[13005]	175
[18775]	176	%dealing with the friciton law
[13692]	177	%drag is limited to nodes that are on the bedrock.
[18775]	178	if isa(md.friction,'friction'),
	179	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	180	md.friction.p=project2d(md,md.friction.p,1);
	181	md.friction.q=project2d(md,md.friction.q,1);
	182	elseif isa(md.friction,'frictionhydro'),
	183	md.friction.q=project2d(md,md.friction.q,1);
	184	md.friction.C=project2d(md,md.friction.C,1);
	185	md.friction.As=project2d(md,md.friction.As,1);
[18798]	186	md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
[18775]	187	elseif isa(md.friction,'frictionwaterlayer'),
	188	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	189	md.friction.p=project2d(md,md.friction.p,1);
	190	md.friction.q=project2d(md,md.friction.q,1);
	191	md.friction.water_layer=project2d(md,md.friction.water_layer,1);
	192	elseif isa(md.friction,'frictionweertman'),
	193	md.friction.C=project2d(md,md.friction.C,1);
	194	md.friction.m=project2d(md,md.friction.m,1);
[19720]	195	elseif isa(md.friction,'frictionweertmantemp'),
	196	md.friction.C=project2d(md,md.friction.C,1);
	197	md.friction.m=project2d(md,md.friction.m,1);
	198	else
	199	disp('friction type not supported');
[18775]	200	end
[13005]	201
[13692]	202	%observations
	203	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
	204	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
	205	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
	206	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
	207	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
	208	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
[19527]	209	if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
	210	md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
	211	elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
	212	md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
[13692]	213	end;
[13005]	214
[13692]	215	%results
	216	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
	217	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
	218	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
	219	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
[18578]	220	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[18506]	221	if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
[18578]	222	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
	223	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
	224	if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
[21417]	225	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
	226	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
[21530]	227	%giaivins
	228	if ~isnan(md.giaivins.mantle_viscosity), md.giaivins.mantle_viscosity=project2d(md,md.giaivins.mantle_viscosity,1); end
	229	if ~isnan(md.giaivins.lithosphere_thickness), md.giaivins.lithosphere_thickness=project2d(md,md.giaivins.lithosphere_thickness,1); end
[15021]	230
[13692]	231	%elementstype
	232	if ~isnan(md.flowequation.element_equation)
	233	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
	234	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]	235	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
	236	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
	237	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]	238	end
[13005]	239
[13692]	240	%boundary conditions
[15771]	241	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
	242	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
	243	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
	244	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
	245	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[15767]	246	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
[21544]	247	if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
[21417]	248	if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
[13692]	249	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]	250
[18506]	251	% Hydrologydc variables
	252	if isa(md.hydrology,'hydrologydc');
	253	md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
	254	md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
	255	md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
	256	md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
	257	if(md.hydrology.isefficientlayer==1)
	258	md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
	259	end
	260	end
	261
[13692]	262	%materials
	263	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
	264	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]	265
	266	%damage:
[17940]	267	if md.damage.isdamage,
	268	md.damage.D=DepthAverage(md,md.damage.D);
	269	end
[13005]	270
[13692]	271	%special for thermal modeling:
[18378]	272	if ~isnan(md.basalforcings.groundedice_melting_rate),
	273	md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
	274	end
[21417]	275	if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
[18378]	276	md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
	277	end
[13692]	278	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]	279
[21417]	280	if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
	281	md.calving.coeff=project2d(md,md.calving.coeff,1);
	282	end
	283	if isprop(md.calving,'meltingrate') & ~isnan(md.calving.meltingrate),
	284	md.calving.meltingrate=project2d(md,md.calving.meltingrate,1);
	285	end
	286
[13692]	287	%update of connectivity matrix
	288	md.mesh.average_vertex_connectivity=25;
[13005]	289
[13692]	290	%Collapse the mesh
	291	nodes2d=md.mesh.numberofvertices2d;
	292	elements2d=md.mesh.numberofelements2d;
[13005]	293
[13692]	294	%parameters
	295	md.geometry.surface=project2d(md,md.geometry.surface,1);
	296	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
[17590]	297	md.geometry.base=project2d(md,md.geometry.base,1);
[18480]	298	if ~isnan(md.geometry.bed),
	299	md.geometry.bed=project2d(md,md.geometry.bed,1);
	300	end
[17991]	301
[18378]	302	if ~isnan(md.mask.groundedice_levelset),
	303	md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
	304	end
	305	if ~isnan(md.mask.ice_levelset),
	306	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
	307	end
[13005]	308
[13692]	309	%Initialize with the 2d mesh
[17724]	310	mesh=mesh2d();
	311	mesh.x=md.mesh.x2d;
	312	mesh.y=md.mesh.y2d;
	313	mesh.numberofvertices=md.mesh.numberofvertices2d;
	314	mesh.numberofelements=md.mesh.numberofelements2d;
	315	mesh.elements=md.mesh.elements2d;
[21499]	316	if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end
	317	if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end
	318	mesh.epsg=md.mesh.epsg;
[17991]	319	if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
	320	if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
[17724]	321	md.mesh=mesh;
[18738]	322	md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
	323	md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
[19955]	324	md.mesh.segments=contourenvelope(md.mesh);
[13005]	325
[13692]	326	end % }}}
	327	function md2 = extract(md,area) % {{{
	328	%extract - extract a model according to an Argus contour or flag list
	329	%
	330	% This routine extracts a submodel from a bigger model with respect to a given contour
	331	% md must be followed by the corresponding exp file or flags list
	332	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
	333	% If user wants every element outside the domain to be
[15564]	334	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]	335	% an empty string '' will be considered as an empty domain
	336	% a string 'all' will be considered as the entire domain
	337	%
	338	% Usage:
	339	% md2=extract(md,area);
	340	%
	341	% Examples:
	342	% md2=extract(md,'Domain.exp');
	343	%
	344	% See also: EXTRUDE, COLLAPSE
[13005]	345
[13692]	346	%copy model
	347	md1=md;
[13005]	348
[13692]	349	%some checks
	350	if ((nargin~=2) \| (nargout~=1)),
	351	help extract
	352	error('extract error message: bad usage');
	353	end
[13005]	354
[13692]	355	%get elements that are inside area
	356	flag_elem=FlagElements(md1,area);
	357	if ~any(flag_elem),
	358	error('extracted model is empty');
	359	end
[13005]	360
[13692]	361	%kick out all elements with 3 dirichlets
	362	spc_elem=find(~flag_elem);
	363	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
	364	flag=ones(md1.mesh.numberofvertices,1);
	365	flag(spc_node)=0;
	366	pos=find(sum(flag(md1.mesh.elements),2)==0);
	367	flag_elem(pos)=0;
[13005]	368
[13692]	369	%extracted elements and nodes lists
	370	pos_elem=find(flag_elem);
	371	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]	372
[13692]	373	%keep track of some fields
	374	numberofvertices1=md1.mesh.numberofvertices;
	375	numberofelements1=md1.mesh.numberofelements;
	376	numberofvertices2=length(pos_node);
	377	numberofelements2=length(pos_elem);
	378	flag_node=zeros(numberofvertices1,1);
	379	flag_node(pos_node)=1;
[13005]	380
[13692]	381	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
	382	Pelem=zeros(numberofelements1,1);
	383	Pelem(pos_elem)=[1:numberofelements2]';
	384	Pnode=zeros(numberofvertices1,1);
	385	Pnode(pos_node)=[1:numberofvertices2]';
[13005]	386
[13857]	387	%renumber the elements (some nodes won't exist anymore)
[13692]	388	elements_1=md1.mesh.elements;
	389	elements_2=elements_1(pos_elem,:);
	390	elements_2(:,1)=Pnode(elements_2(:,1));
	391	elements_2(:,2)=Pnode(elements_2(:,2));
	392	elements_2(:,3)=Pnode(elements_2(:,3));
[17558]	393	if isa(md1.mesh,'mesh3dprisms'),
[13692]	394	elements_2(:,4)=Pnode(elements_2(:,4));
	395	elements_2(:,5)=Pnode(elements_2(:,5));
	396	elements_2(:,6)=Pnode(elements_2(:,6));
	397	end
[13005]	398
[13857]	399	%OK, now create the new model!
[13005]	400
[13857]	401	%take every field from model
[13692]	402	md2=md1;
[13005]	403
[13692]	404	%automatically modify fields
[13005]	405
[13692]	406	%loop over model fields
	407	model_fields=fields(md1);
	408	for i=1:length(model_fields),
	409	%get field
	410	field=md1.(model_fields{i});
	411	fieldsize=size(field);
	412	if isobject(field), %recursive call
	413	object_fields=fields(md1.(model_fields{i}));
	414	for j=1:length(object_fields),
	415	%get field
	416	field=md1.(model_fields{i}).(object_fields{j});
	417	fieldsize=size(field);
	418	%size = number of nodes * n
	419	if fieldsize(1)==numberofvertices1
	420	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
	421	elseif (fieldsize(1)==numberofvertices1+1)
	422	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]	423	%size = number of elements * n
[13692]	424	elseif fieldsize(1)==numberofelements1
	425	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
[21428]	426	elseif (fieldsize(1)==numberofelements1+1)
	427	md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
[13692]	428	end
	429	end
	430	else
	431	%size = number of nodes * n
	432	if fieldsize(1)==numberofvertices1
	433	md2.(model_fields{i})=field(pos_node,:);
	434	elseif (fieldsize(1)==numberofvertices1+1)
	435	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]	436	%size = number of elements * n
[13692]	437	elseif fieldsize(1)==numberofelements1
	438	md2.(model_fields{i})=field(pos_elem,:);
[21428]	439	elseif (fieldsize(1)==numberofelements1+1)
	440	md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
[13692]	441	end
	442	end
	443	end
[13005]	444
[13692]	445	%modify some specific fields
[13005]	446
[13692]	447	%Mesh
	448	md2.mesh.numberofelements=numberofelements2;
	449	md2.mesh.numberofvertices=numberofvertices2;
	450	md2.mesh.elements=elements_2;
[13005]	451
[13692]	452	%mesh.uppervertex mesh.lowervertex
[17558]	453	if isa(md1.mesh,'mesh3dprisms'),
[13692]	454	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
	455	pos=find(~isnan(md2.mesh.uppervertex));
	456	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]	457
[13692]	458	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
	459	pos=find(~isnan(md2.mesh.lowervertex));
	460	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]	461
[13692]	462	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
	463	pos=find(~isnan(md2.mesh.upperelements));
	464	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]	465
[13692]	466	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
	467	pos=find(~isnan(md2.mesh.lowerelements));
	468	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
	469	end
[13005]	470
[13692]	471	%Initial 2d mesh
[17558]	472	if isa(md1.mesh,'mesh3dprisms'),
[13692]	473	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
	474	pos_elem_2d=find(flag_elem_2d);
	475	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
	476	pos_node_2d=find(flag_node_2d);
[13005]	477
[13692]	478	md2.mesh.numberofelements2d=length(pos_elem_2d);
	479	md2.mesh.numberofvertices2d=length(pos_node_2d);
	480	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
	481	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
	482	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
	483	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]	484
[13692]	485	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
	486	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
	487	end
[13005]	488
[13692]	489	%Edges
[17686]	490	if(dimension(md.mesh)==2),
[17563]	491	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
	492	%renumber first two columns
	493	pos=find(md2.mesh.edges(:,4)~=-1);
	494	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
	495	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
	496	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
	497	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
	498	%remove edges when the 2 vertices are not in the domain.
	499	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
	500	%Replace all zeros by -1 in the last two columns
	501	pos=find(md2.mesh.edges(:,3)==0);
	502	md2.mesh.edges(pos,3)=-1;
	503	pos=find(md2.mesh.edges(:,4)==0);
	504	md2.mesh.edges(pos,4)=-1;
	505	%Invert -1 on the third column with last column (Also invert first two columns!!)
	506	pos=find(md2.mesh.edges(:,3)==-1);
	507	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
	508	md2.mesh.edges(pos,4)=-1;
	509	values=md2.mesh.edges(pos,2);
	510	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
	511	md2.mesh.edges(pos,1)=values;
	512	%Finally remove edges that do not belong to any element
	513	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
	514	md2.mesh.edges(pos,:)=[];
	515	end
[13692]	516	end
[13005]	517
[13692]	518	%Penalties
[15771]	519	if ~isnan(md2.stressbalance.vertex_pairing),
	520	for i=1:size(md1.stressbalance.vertex_pairing,1);
	521	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]	522	end
[15771]	523	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]	524	end
[15767]	525	if ~isnan(md2.masstransport.vertex_pairing),
	526	for i=1:size(md1.masstransport.vertex_pairing,1);
	527	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]	528	end
[15767]	529	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]	530	end
[13005]	531
[13692]	532	%recreate segments
[20322]	533	if isa(md1.mesh,'mesh2d') \| isa(md1.mesh','mesh3dsurface'),
[13692]	534	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	535	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
[19957]	536	md2.mesh.segments=contourenvelope(md2.mesh);
[13692]	537	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
	538	else
	539	%First do the connectivity for the contourenvelope in 2d
	540	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
	541	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
[19957]	542	segments=contourenvelope(md2.mesh);
[17565]	543	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
[13692]	544	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
	545	%Then do it for 3d as usual
	546	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	547	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	548	end
[13005]	549
[13692]	550	%Boundary conditions: Dirichlets on new boundary
	551	%Catch the elements that have not been extracted
	552	orphans_elem=find(~flag_elem);
	553	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
	554	%Figure out which node are on the boundary between md2 and md1
	555	nodestoflag1=intersect(orphans_node,pos_node);
	556	nodestoflag2=Pnode(nodestoflag1);
[15771]	557	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
[13692]	558	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]	559	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
	560	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]	561	else
[15771]	562	md2.stressbalance.spcvx(nodestoflag2)=NaN;
	563	md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]	564	disp(' ')
	565	disp('!! extract warning: spc values should be checked !!')
	566	disp(' ')
	567	end
	568	%put 0 for vz
[15771]	569	md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]	570	end
	571	if ~isnan(md1.thermal.spctemperature),
	572	md2.thermal.spctemperature(nodestoflag2,1)=1;
	573	end
[13005]	574
[13692]	575	%Results fields
	576	if isstruct(md1.results),
	577	md2.results=struct();
	578	solutionfields=fields(md1.results);
	579	for i=1:length(solutionfields),
[14230]	580	if isstruct(md1.results.(solutionfields{i}))
	581	%get subfields
	582	solutionsubfields=fields(md1.results.(solutionfields{i}));
	583	for j=1:length(solutionsubfields),
	584	field=md1.results.(solutionfields{i}).(solutionsubfields{j});
	585	if length(field)==numberofvertices1,
	586	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
	587	elseif length(field)==numberofelements1,
	588	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
	589	else
	590	md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
	591	end
	592	end
	593	else
	594	field=md1.results.(solutionfields{i});
[13692]	595	if length(field)==numberofvertices1,
[14230]	596	md2.results.(solutionfields{i})=field(pos_node);
[13692]	597	elseif length(field)==numberofelements1,
[14230]	598	md2.results.(solutionfields{i})=field(pos_elem);
[13692]	599	else
[14230]	600	md2.results.(solutionfields{i})=field;
[13692]	601	end
	602	end
	603	end
	604	end
[13005]	605
[13692]	606	%Keep track of pos_node and pos_elem
	607	md2.mesh.extractedvertices=pos_node;
	608	md2.mesh.extractedelements=pos_elem;
	609	end % }}}
	610	function md = extrude(md,varargin) % {{{
	611	%EXTRUDE - vertically extrude a 2d mesh
	612	%
	613	% vertically extrude a 2d mesh and create corresponding 3d mesh.
	614	% The vertical distribution can:
	615	% - follow a polynomial law
	616	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
	617	% - be discribed by a list of coefficients (between 0 and 1)
	618	%
	619	%
	620	% Usage:
	621	% md=extrude(md,numlayers,extrusionexponent);
	622	% md=extrude(md,numlayers,lowerexponent,upperexponent);
	623	% md=extrude(md,listofcoefficients);
	624	%
	625	% Example:
[18216]	626	% md=extrude(md,15,1.3);
	627	% md=extrude(md,15,1.3,1.2);
[13692]	628	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
	629	%
	630	% See also: MODELEXTRACT, COLLAPSE
[13005]	631
[13692]	632	%some checks on list of arguments
	633	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
	634	help extrude;
	635	error('extrude error message');
	636	end
[13005]	637
[13692]	638	%Extrude the mesh
	639	if nargin==2, %list of coefficients
	640	clist=varargin{1};
	641	if any(clist<0) \| any(clist>1),
	642	error('extrusioncoefficients must be between 0 and 1');
	643	end
	644	extrusionlist=sort(unique([clist(:);0;1]));
	645	numlayers=length(extrusionlist);
	646	elseif nargin==3, %one polynomial law
	647	if varargin{2}<=0,
	648	help extrude;
	649	error('extrusionexponent must be >=0');
	650	end
	651	numlayers=varargin{1};
	652	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
	653	elseif nargin==4, %two polynomial laws
	654	numlayers=varargin{1};
	655	lowerexp=varargin{2};
	656	upperexp=varargin{3};
[13005]	657
[13692]	658	if varargin{2}<=0 \| varargin{3}<=0,
	659	help extrude;
	660	error('lower and upper extrusionexponents must be >=0');
	661	end
[13005]	662
[13692]	663	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
	664	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
	665	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]	666
[13692]	667	end
[13005]	668
[13692]	669	if numlayers<2,
	670	error('number of layers should be at least 2');
	671	end
[17686]	672	if strcmp(md.mesh.domaintype(),'3D')
[13692]	673	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
	674	end
[13005]	675
[13692]	676	%Initialize with the 2d mesh
[17558]	677	mesh2d = md.mesh;
	678	md.mesh=mesh3dprisms();
	679	md.mesh.x = mesh2d.x;
	680	md.mesh.y = mesh2d.y;
	681	md.mesh.elements = mesh2d.elements;
	682	md.mesh.numberofelements = mesh2d.numberofelements;
	683	md.mesh.numberofvertices = mesh2d.numberofvertices;
	684
	685	md.mesh.lat = mesh2d.lat;
	686	md.mesh.long = mesh2d.long;
[18558]	687	md.mesh.epsg = mesh2d.epsg;
[17558]	688
	689	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
	690	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
	691	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
	692	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
	693
	694	md.mesh.extractedvertices = mesh2d.extractedvertices;
	695	md.mesh.extractedelements = mesh2d.extractedelements;
	696
[13692]	697	x3d=[];
	698	y3d=[];
	699	z3d=[]; %the lower node is on the bed
	700	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
[17590]	701	bed3d=md.geometry.base;
[13005]	702
[13692]	703	%Create the new layers
	704	for i=1:numlayers,
	705	x3d=[x3d; md.mesh.x];
	706	y3d=[y3d; md.mesh.y];
	707	%nodes are distributed between bed and surface accordingly to the given exponent
	708	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
	709	end
	710	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	711
[13692]	712	%Extrude elements
	713	elements3d=[];
	714	for i=1:numlayers-1,
	715	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
	716	end
	717	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	718
[13692]	719	%Keep a trace of lower and upper nodes
[17590]	720	lowervertex=NaN*ones(number_nodes3d,1);
	721	uppervertex=NaN*ones(number_nodes3d,1);
	722	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
	723	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
	724	md.mesh.lowervertex=lowervertex;
	725	md.mesh.uppervertex=uppervertex;
[13005]	726
[13692]	727	%same for lower and upper elements
[17590]	728	lowerelements=NaN*ones(number_el3d,1);
	729	upperelements=NaN*ones(number_el3d,1);
	730	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
	731	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
	732	md.mesh.lowerelements=lowerelements;
	733	md.mesh.upperelements=upperelements;
[13005]	734
[13692]	735	%Save old mesh
	736	md.mesh.x2d=md.mesh.x;
	737	md.mesh.y2d=md.mesh.y;
	738	md.mesh.elements2d=md.mesh.elements;
	739	md.mesh.numberofelements2d=md.mesh.numberofelements;
	740	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]	741
[13692]	742	%Build global 3d mesh
	743	md.mesh.elements=elements3d;
	744	md.mesh.x=x3d;
	745	md.mesh.y=y3d;
	746	md.mesh.z=z3d;
	747	md.mesh.numberofelements=number_el3d;
	748	md.mesh.numberofvertices=number_nodes3d;
	749	md.mesh.numberoflayers=numlayers;
[13005]	750
[13692]	751	%Ok, now deal with the other fields from the 2d mesh:
[13005]	752
[19048]	753	%bedinfo and surface info
	754	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
	755	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
	756	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
	757
[13692]	758	%lat long
	759	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
	760	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[13005]	761
[19048]	762	md.geometry=extrude(md.geometry,md);
	763	md.friction = extrude(md.friction,md);
	764	md.inversion = extrude(md.inversion,md);
[19527]	765	md.smb = extrude(md.smb,md);
[19048]	766	md.initialization = extrude(md.initialization,md);
[13005]	767
[19050]	768	md.flowequation=md.flowequation.extrude(md);
[19048]	769	md.stressbalance=extrude(md.stressbalance,md);
[19050]	770	md.thermal=md.thermal.extrude(md);
	771	md.masstransport=md.masstransport.extrude(md);
[20460]	772	md.levelset=extrude(md.levelset,md);
[19048]	773	md.calving=extrude(md.calving,md);
	774	md.hydrology = extrude(md.hydrology,md);
[13005]	775
[13692]	776	%connectivity
[17991]	777	if ~isnan(md.mesh.elementconnectivity)
	778	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
	779	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
	780	for i=2:numlayers-1,
	781	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
	782	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
	783	end
	784	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13692]	785	end
[13005]	786
[19048]	787	md.materials=extrude(md.materials,md);
	788	md.damage=extrude(md.damage,md);
	789	md.mask=extrude(md.mask,md);
	790	md.qmu=extrude(md.qmu,md);
	791	md.basalforcings=extrude(md.basalforcings,md);
[13005]	792
[13692]	793	%increase connectivity if less than 25:
	794	if md.mesh.average_vertex_connectivity<=25,
	795	md.mesh.average_vertex_connectivity=100;
	796	end
[13005]	797	end % }}}
[13692]	798	function md = structtomodel(md,structmd) % {{{
[8952]	799
[13692]	800	if ~isstruct(structmd) error('input model is not a structure'); end
[8952]	801
[13692]	802	%loaded model is a struct, initialize output and recover all fields
	803	md = structtoobj(model,structmd);
[8952]	804
[13692]	805	%Old field now classes
	806	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
	807	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]	808
[13692]	809	%Field name change
	810	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	811	if isfield(structmd,'p'), md.friction.p=structmd.p; end
	812	if isfield(structmd,'q'), md.friction.q=structmd.p; end
[18378]	813	if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
[18068]	814	if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
[18378]	815	if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
[19527]	816	if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
[13692]	817	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
	818	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
	819	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
	820	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
[17610]	821	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
[13692]	822	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
	823	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
	824	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]	825	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]	826	if isfield(structmd,'g'), md.constants.g=structmd.g; end
	827	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
[19527]	828	if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
[18068]	829	if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
[13692]	830	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
	831	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	832	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
	833	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
	834	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
	835	if isfield(structmd,'riftproperties'), %old implementation
	836	md.rifts=rifts();
	837	md.rifts.riftproperties=structmd.riftproperties;
	838	md.rifts.riftstruct=structmd.rifts;
	839	md.rifts.riftproperties=structmd.riftinfo;
	840	end
	841	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
	842	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
	843	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
	844	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
	845	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
	846	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
	847	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
	848	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
	849	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
	850	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
	851	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
	852	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
	853	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
	854	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
	855	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
	856	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
	857	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
	858	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
	859	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
	860	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
	861	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
	862	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]	863	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
	864	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
	865	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
	866	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
	867	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]	868	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
	869	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
	870	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
	871	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]	872	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]	873	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
	874	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
	875	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]	876	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
	877	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]	878	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
	879	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
	880	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
	881	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]	882	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]	883	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]	884	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
	885	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
	886	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
	887	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
	888	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
	889	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
	890	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
	891	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
	892	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
	893	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
	894	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
	895	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
	896	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
	897	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
	898	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
	899	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
	900	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
	901	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
	902	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
	903	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
[17590]	904	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
[13692]	905	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
[17590]	906	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
[13692]	907	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
	908	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
	909	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
	910	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
	911	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
	912	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
	913	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
	914	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
	915	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
	916	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
	917	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
	918	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
	919	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
	920	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
	921	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
	922	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
	923	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
	924	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
	925	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
	926	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
	927	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
	928	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
	929	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
[17610]	930	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
[13692]	931	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
	932	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
	933	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
	934	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]	935	if isfield(structmd,'edges'),
	936	md.mesh.edges=structmd.edges;
	937	md.mesh.edges(isnan(md.mesh.edges))=-1;
	938	end
[13692]	939	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
	940	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
	941	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
[15771]	942	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]	943	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
	944	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]	945
[13692]	946	if isnumeric(md.verbose),
	947	md.verbose=verbose;
	948	end
[15768]	949
[13692]	950	if isfield(structmd,'spcvelocity'),
[15771]	951	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	952	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	953	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	954	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
	955	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
	956	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]	957	end
	958	if isfield(structmd,'spcvx'),
[15771]	959	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	960	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]	961	end
	962	if isfield(structmd,'spcvy'),
[15771]	963	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	964	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]	965	end
	966	if isfield(structmd,'spcvz'),
[15771]	967	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	968	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]	969	end
[14620]	970	if isfield(structmd,'pressureload'),
	971	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]	972	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
	973	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
	974	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]	975	end
[13692]	976	end
	977	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
	978	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
	979	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
	980	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
	981	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
	982	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
	983	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
	984	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
	985	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
	986	end
	987	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
	988	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
	989	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
	990	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
	991	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
	992	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
	993	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
	994	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
	995	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
	996	end
	997	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
	998	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
	999	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
	1000	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
	1001	end
	1002	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
	1003	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
[17941]	1004	if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
[13692]	1005	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
	1006	end
	1007	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
	1008	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
	1009	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
	1010	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
	1011	end
	1012	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
	1013	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
	1014	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
	1015	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
	1016	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
	1017	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
	1018	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
	1019	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
	1020	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
	1021	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
	1022	end
[11659]	1023
[13692]	1024	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
	1025	md.thermal.stabilization=2;
[15767]	1026	md.masstransport.stabilization=1;
[13692]	1027	md.balancethickness.stabilization=1;
	1028	end
[15767]	1029	if isnumeric(md.masstransport.hydrostatic_adjustment)
	1030	if md.masstransport.hydrostatic_adjustment==269,
	1031	md.masstransport.hydrostatic_adjustment='Incremental';
[13692]	1032	else
[15767]	1033	md.masstransport.hydrostatic_adjustment='Absolute';
[13692]	1034	end
	1035	end
[8952]	1036
[13692]	1037	%New fields
[19124]	1038	if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1039	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
	1040	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
	1041	end
[19124]	1042	if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1043	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
	1044	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
	1045	end
	1046	if ~isfield(structmd,'diagnostic_ref');
[15771]	1047	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]	1048	end
[14529]	1049	if ~isfield(structmd,'loadingforce');
[15771]	1050	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]	1051	end
[15768]	1052
	1053	%2013 August 9
	1054	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
	1055	disp('Recovering old prognostic class');
	1056	md.masstransport=masstransport(structmd.prognostic);
	1057	end
[15771]	1058	%2013 August 9
[15775]	1059	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
[15771]	1060	disp('Recovering old diagnostic class');
[15775]	1061	md.stressbalance=stressbalance(structmd.diagnostic);
[15771]	1062	end
[19642]	1063	%2014 January 9th
[21148]	1064	if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
[19642]	1065	disp('Recovering old surfaceforcings class');
	1066	mass_balance=structmd.surfaceforcings.mass_balance;
	1067	md.smb=SMB();
	1068	md.smb.mass_balance=mass_balance;
	1069	end
	1070	%2015 September 10
[21148]	1071	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
[19642]	1072	disp('Recovering old SMB class');
	1073	md.smb=SMBforcing(structmd.surfaceforcings);
	1074	end
[21148]	1075	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
	1076	disp('Recovering old SMBhenning class');
	1077	md.smb=SMBhenning(structmd.surfaceforcings);
	1078	end
[19642]	1079
[13692]	1080	end% }}}
	1081	function md = setdefaultparameters(md) % {{{
[8926]	1082
[13692]	1083	%initialize subclasses
[17558]	1084	md.mesh = mesh2d();
[13692]	1085	md.mask = mask();
	1086	md.constants = constants();
	1087	md.geometry = geometry();
	1088	md.initialization = initialization();
[19527]	1089	md.smb = SMBforcing();
[13692]	1090	md.basalforcings = basalforcings();
	1091	md.friction = friction();
	1092	md.rifts = rifts();
[19984]	1093	md.slr = slr();
[13692]	1094	md.timestepping = timestepping();
	1095	md.groundingline = groundingline();
	1096	md.materials = matice();
[16160]	1097	md.damage = damage();
[13692]	1098	md.flowequation = flowequation();
	1099	md.debug = debug();
[14558]	1100	md.verbose = verbose();
[13692]	1101	md.settings = settings();
[17932]	1102	md.toolkits = toolkits();
[13692]	1103	md.cluster = generic();
	1104	md.balancethickness = balancethickness();
[17079]	1105	md.stressbalance = stressbalance();
[14555]	1106	md.hydrology = hydrologyshreve();
[17079]	1107	md.masstransport = masstransport();
[13692]	1108	md.thermal = thermal();
	1109	md.steadystate = steadystate();
	1110	md.transient = transient();
[20460]	1111	md.levelset = levelset();
[18757]	1112	md.calving = calving();
[21544]	1113	md.giaivins = giaivins();
[21260]	1114	md.esa = esa();
[13692]	1115	md.autodiff = autodiff();
	1116	md.inversion = inversion();
	1117	md.qmu = qmu();
	1118	md.radaroverlay = radaroverlay();
	1119	md.results = struct();
[16388]	1120	md.outputdefinition = outputdefinition();
[13692]	1121	md.miscellaneous = miscellaneous();
	1122	md.private = private();
	1123	end
	1124	%}}}
[17483]	1125	function md = tetras(md,varargin) % {{{
	1126	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
	1127	%
	1128	% Usage:
	1129	% md=tetra(md)
	1130
	1131	if ~isa(md.mesh,'mesh3dprisms')
	1132	error('mesh is not a 3d prismatic mesh');
	1133	end
	1134
	1135	%Initialize tetra mesh
	1136	md.mesh=mesh3dtetras(md.mesh);
	1137
[17754]	1138	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
	1139	steiner = 0;
	1140	nbv = md.mesh.numberofvertices;
	1141	nbt = 3*md.mesh.numberofelements;
	1142	elements = zeros(nbt,4);
	1143	for i=1:md.mesh.numberofelements
	1144	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
	1145	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
	1146	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1147	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1148	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1149	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1150	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1151	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1152	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
	1153	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
	1154	elements(end+1,:) = [v2 v3 v5 v7];
	1155	elements(end+1,:) = [v3 v5 v6 v7];
	1156	elements(end+1,:) = [v1 v3 v6 v7];
	1157	elements(end+1,:) = [v1 v4 v6 v7];
	1158	elements(end+1,:) = [v4 v5 v6 v7];
	1159	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1160	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
	1161	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1162	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1163	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1164	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1165	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
	1166	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1167	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1168	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1169	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1170	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
[18142]	1171	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
[17754]	1172	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1173	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1174	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
	1175	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1176	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1177	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
	1178	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1179	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1180	elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
	1181	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1182	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1183	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1184	elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
	1185	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1186	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
	1187	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1188	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1189	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1190	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1191	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1192	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1193	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
	1194	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
	1195	elements(end+1,:) = [v2 v5 v6 v7];
	1196	elements(end+1,:) = [v2 v3 v6 v7];
	1197	elements(end+1,:) = [v3 v4 v6 v7];
	1198	elements(end+1,:) = [v1 v3 v4 v7];
	1199	elements(end+1,:) = [v4 v5 v6 v7];
	1200	else
	1201	error('Case not supported'); %not supposed to happen!
	1202	end
[17774]	1203	%Reorder elements to make sure they are direct
	1204	for j=1:3
	1205	element = elements(3*(i-1)+j,:);
	1206	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
	1207	if det(matrix)>0,
	1208	elements(3*(i-1)+j,1)=element(2);
	1209	elements(3*(i-1)+j,2)=element(1);
	1210	end
	1211	end
[17754]	1212	end
	1213	%%Split in 3 tetras
	1214	%subelement1 = [1 2 3 5];
	1215	%subelement2 = [4 6 5 1];
	1216	%subelement3 = [5 6 3 1];
	1217	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
[17774]	1218	if steiner==0,
	1219	disp('No Steiner point required to split prismatic mesh into tets');
	1220	else
	1221	disp([num2str(steiner) ' Steiner points had to be included'])
	1222	error('Steiner point not supported yet');
	1223	end
[17754]	1224
[17483]	1225	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
	1226
	1227	md.mesh.elements=elements;
	1228	md.mesh.numberofelements=size(elements,1);
	1229
	1230	%p and q (same deal, except for element that are on the bedrock: )
[17774]	1231	if ~isnan(md.friction.p),
	1232	md.friction.p=md.friction.p(pos_elements);
	1233	md.friction.q=md.friction.q(pos_elements);
	1234	end
[17483]	1235
	1236	%elementstype
	1237	if ~isnan(md.flowequation.element_equation)
	1238	oldelements_type=md.flowequation.element_equation;
	1239	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
	1240	end
	1241
	1242	%connectivity
	1243	md.mesh.elementconnectivity=NaN;
	1244
	1245	%materials
[17774]	1246	if ~isnan(md.materials.rheology_n),
	1247	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
	1248	end
[17483]	1249
	1250	%increase connectivity if less than 25:
	1251	if md.mesh.average_vertex_connectivity<=25,
	1252	md.mesh.average_vertex_connectivity=100;
	1253	end
	1254	end % }}}
[19040]	1255	function disp(self) % {{{
	1256	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
	1257	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
	1258	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
	1259	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
[19527]	1260	disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
[19040]	1261	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
	1262	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
	1263	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
	1264	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
	1265	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
	1266	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
	1267	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
	1268	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
[19984]	1269	disp(sprintf('%19s: %-22s -- %s','slr' ,['[1x1 ' class(self.slr) ']'],'slr forcings'));
[19040]	1270	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
	1271	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
	1272	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
	1273	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
	1274	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
	1275	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
	1276	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
	1277	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
	1278	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
	1279	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
	1280	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
	1281	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
	1282	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
[21544]	1283	disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
[19040]	1284	disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
[21544]	1285	disp(sprintf('%19s: %-22s -- %s','giaivins' ,['[1x1 ' class(self.giaivins) ']'],'parameters for giaivins solution'));
[21260]	1286	disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
[19040]	1287	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
	1288	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
	1289	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
	1290	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
	1291	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
	1292	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
	1293	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
[13692]	1294	end % }}}
[19040]	1295	function memory(self) % {{{
[15106]	1296
[14611]	1297	disp(sprintf('\nMemory imprint:\n'));
[14307]	1298
[14603]	1299	fields=properties('model');
	1300	mem=0;
[15106]	1301
[14603]	1302	for i=1:length(fields),
[19040]	1303	field=self.(fields{i});
[14603]	1304	s=whos('field');
	1305	mem=mem+s.bytes/1e6;
[14611]	1306	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]	1307	end
[14603]	1308	disp(sprintf('%19s--%10s','--------------','--------------'));
	1309	disp(sprintf('%19s: %g Mb','Total',mem));
[14307]	1310	end % }}}
[19040]	1311	function netcdf(self,filename) % {{{
[14603]	1312	%NETCDF - save model as netcdf
	1313	%
	1314	% Usage:
	1315	% netcdf(md,filename)
	1316	%
	1317	% Example:
	1318	% netcdf(md,'model.nc');
	1319
	1320	disp('Saving model as NetCDF');
	1321	%1. Create NetCDF file
	1322	ncid=netcdf.create(filename,'CLOBBER');
	1323	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[19040]	1324	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
[14603]	1325	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
	1326	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
	1327
[14611]	1328	%Preallocate variable id, needed to write variables in netcdf file
[14631]	1329	var_id=zeros(1000,1);%preallocate
[14609]	1330
	1331	for step=1:2,
	1332	counter=0;
[19040]	1333	[var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
[14609]	1334	if step==1, netcdf.endDef(ncid); end
[14603]	1335	end
[14611]	1336
[14631]	1337	if counter>1000,
	1338	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]	1339	end
	1340
	1341	netcdf.close(ncid)
[14603]	1342	end % }}}
[19040]	1343	function xylim(self) % {{{
[14405]	1344
[19040]	1345	xlim([min(self.mesh.x) max(self.mesh.x)]);
	1346	ylim([min(self.mesh.y) max(self.mesh.y)])
[14405]	1347	end % }}}
[15316]	1348	function md=upload(md) % {{{
	1349	%the goal of this routine is to upload the model onto a server, and to empty it.
	1350	%So first, save the model with a unique name and upload the file to the server:
	1351	random_part=fix(rand(1)*10000);
	1352	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
	1353	eval(['save ' id ' md']);
	1354
	1355	%Now, upload the file:
	1356	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
	1357
	1358	%Now, empty this model of everything except settings, and record name of file we just uploaded!
	1359	settings_back=md.settings;
	1360	md=model();
	1361	md.settings=settings_back;
	1362	md.settings.upload_filename=id;
	1363
	1364	%get locally rid of file that was uploaded
	1365	eval(['delete ' id]);
	1366
	1367	end % }}}
	1368	function md=download(md) % {{{
[15643]	1369
[15316]	1370	%the goal of this routine is to download the internals of the current model from a server, because
	1371	%this model is empty, except for the settings which tell us where to go and find this model!
[15643]	1372
[15316]	1373	%Download the file:
	1374	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
	1375
	1376	name=md.settings.upload_filename;
	1377
	1378	%Now, load this model:
	1379	md=loadmodel(md.settings.upload_filename);
	1380
	1381	%get locally rid of file that was downloaded
	1382	eval(['delete ' name]);
	1383
	1384	end % }}}
[19894]	1385	function savemodeljs(md,modelname,websiteroot) % {{{
[19879]	1386
	1387	%the goal of this routine is to save the model as a javascript array that can be included in any html
	1388	%file:
	1389
	1390	%disp:
[19894]	1391	disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
[19879]	1392
	1393	%open file for writing and declare the model:
[19894]	1394	fid=fopen([websiteroot '/js/' modelname '.js'],'w');
[19879]	1395	fprintf(fid,'var %s=new model();\n',modelname);
	1396
	1397	%now go through all the classes and fwrite all the corresponding fields:
	1398
	1399	fields=properties('model');
	1400	for i=1:length(fields),
	1401	field=fields{i};
	1402
	1403	%Some properties do not need to be saved
[19894]	1404	if ismember(field,{'results','cluster' }),
[19879]	1405	continue;
	1406	end
	1407
	1408	%Check that current field is an object
	1409	if ~isobject(md.(field))
	1410	error(['field ''' char(field) ''' is not an object']);
	1411	end
	1412
	1413	%savemodeljs for current object
	1414	%disp(['javascript saving ' field '...']);
	1415	savemodeljs(md.(field),fid,modelname);
	1416	end
	1417
	1418	%done, close file:
	1419	fclose(fid);
	1420	end
[13692]	1421	end
[8926]	1422	end

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