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source: issm/trunk-jpl/src/m/classes/model.m@ 19642

Last change on this file since 19642 was 19642, checked in by schlegel, 9 years ago
CHG: update lonestar time plus SMBforcing conversions
File size: 61.9 KB

Rev	Line
[8926]	1	%MODEL class definition
	2	%
	3	% Usage:
	4	% md = model(varargin)
	5
	6	classdef model
[13692]	7	properties (SetAccess=public) %Model fields
	8	% {{{
	9	%Careful here: no other class should be used as default value this is a bug of matlab
	10	mesh = 0;
	11	mask = 0;
[9778]	12
[13692]	13	geometry = 0;
	14	constants = 0;
[19527]	15	smb = 0;
[13692]	16	basalforcings = 0;
	17	materials = 0;
[16160]	18	damage = 0;
[13692]	19	friction = 0;
	20	flowequation = 0;
	21	timestepping = 0;
	22	initialization = 0;
	23	rifts = 0;
[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;
[18757]	39	calving = 0;
[14724]	40	gia = 0;
[9778]	41
[13692]	42	autodiff = 0;
	43	flaim = 0;
	44	inversion = 0;
	45	qmu = 0;
[8926]	46
[13692]	47	results = 0;
[16388]	48	outputdefinition = 0;
[13692]	49	radaroverlay = 0;
	50	miscellaneous = 0;
	51	private = 0;
[9778]	52
[13692]	53	%}}}
	54	end
	55	methods (Static)
	56	function md = loadobj(md) % {{{
	57	% This function is directly called by matlab when a model object is
	58	% loaded. If the input is a struct it is an old version of model and
	59	% old fields must be recovered (make sure they are in the deprecated
	60	% model properties)
[8926]	61
[13692]	62	if verLessThan('matlab','7.9'),
	63	disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
	64	disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
[8952]	65
[13692]	66	% This is a Matlab bug: all the fields of md have their default value
	67	% Example of error message:
	68	% Warning: Error loading an object of class 'model':
	69	% Undefined function or method 'exist' for input arguments of type 'cell'
	70	%
	71	% This has been fixed in MATLAB 7.9 (R2009b) and later versions
	72	end
[8952]	73
[13692]	74	if isstruct(md)
	75	disp('Recovering model object from a previous version');
	76	md = structtomodel(model,md);
	77	end
[13239]	78
[13692]	79	%2012 August 4th
	80	if isa(md.materials,'materials'),
	81	disp('Recovering old materials');
	82	if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
[13718]	83	md.materials=matice(md.materials);
	84	else
[13692]	85	md.materials=matdamageice(md.materials);
	86	end
	87	end
[14559]	88	%2013 April 12
[15771]	89	if numel(md.stressbalance.loadingforce==1)
	90	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14559]	91	end
[14618]	92	%2013 April 17
	93	if isa(md.hydrology,'hydrology'),
	94	disp('Recovering old hydrology class');
	95	md.hydrology=hydrologyshreve(md.materials);
	96	end
[16356]	97	%2013 October 9
	98	if ~isa(md.damage,'damage'),
	99	md.damage=damage();
	100	md.damage.D=zeros(md.mesh.numberofvertices,1);
	101	md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
	102	end
[16822]	103	%2013 November 18
	104	if ~isa(md.outputdefinition,'outputdefinition'),
	105	md.outputdefinition=outputdefinition();
	106	end
[17558]	107	%2014 March 26th
	108	if isa(md.mesh,'mesh'),
[17566]	109	disp('Recovering old mesh class');
	110	if isprop(md.mesh,'dimension'),
	111	if md.mesh.dimension==2,
	112	md.mesh=mesh2d(md.mesh);
	113	else
	114	md.mesh=mesh3dprisms(md.mesh);
	115	end
[17558]	116	else
[17566]	117	md.mesh=mesh2dvertical(md.mesh);
[17558]	118	end
	119	end
[18775]	120	%2014 November 12
	121	if isa(md.calving,'double');
	122	md.calving=calving();
	123	end
[13692]	124	end% }}}
	125	end
	126	methods
	127	function md = model(varargin) % {{{
[8926]	128
[13692]	129	switch nargin
	130	case 0
	131	md=setdefaultparameters(md);
[18492]	132	case 1
[19087]	133	error('model constructor not supported yet');
[18503]	134
[13692]	135	otherwise
	136	error('model constructor error message: 0 of 1 argument only in input.');
	137	end
	138	end
	139	%}}}
	140	function md = checkmessage(md,string) % {{{
	141	if(nargout~=1) error('wrong usage, model must be an output'); end
	142	disp(['model not consistent: ' string]);
	143	md.private.isconsistent=false;
	144	end
	145	%}}}
	146	function md = collapse(md)% {{{
	147	%COLLAPSE - collapses a 3d mesh into a 2d mesh
	148	%
	149	% This routine collapses a 3d model into a 2d model
	150	% and collapses all the fileds of the 3d model by
	151	% taking their depth-averaged values
	152	%
	153	% Usage:
	154	% md=collapse(md)
	155	%
	156	% See also: EXTRUDE, MODELEXTRACT
[13005]	157
[13692]	158	%Check that the model is really a 3d model
[17687]	159	if ~strcmp(md.mesh.elementtype(),'Penta'),
[13692]	160	error('collapse error message: only 3d mesh can be collapsed')
	161	end
[13005]	162
[17724]	163	%Start with changing all the fields from the 3d mesh
[13005]	164
[18775]	165	%dealing with the friciton law
[13692]	166	%drag is limited to nodes that are on the bedrock.
[18775]	167	if isa(md.friction,'friction'),
	168	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	169	md.friction.p=project2d(md,md.friction.p,1);
	170	md.friction.q=project2d(md,md.friction.q,1);
	171	elseif isa(md.friction,'frictionhydro'),
	172	md.friction.q=project2d(md,md.friction.q,1);
	173	md.friction.C=project2d(md,md.friction.C,1);
	174	md.friction.As=project2d(md,md.friction.As,1);
[18798]	175	md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
[18775]	176	elseif isa(md.friction,'frictionwaterlayer'),
	177	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	178	md.friction.p=project2d(md,md.friction.p,1);
	179	md.friction.q=project2d(md,md.friction.q,1);
	180	md.friction.water_layer=project2d(md,md.friction.water_layer,1);
	181	elseif isa(md.friction,'frictionweertman'),
	182	md.friction.C=project2d(md,md.friction.C,1);
	183	md.friction.m=project2d(md,md.friction.m,1);
	184	end
[13005]	185
[13692]	186	%observations
	187	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
	188	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
	189	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
	190	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
	191	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
	192	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
[19527]	193	if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
	194	md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
	195	elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
	196	md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
[13692]	197	end;
	198	if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
[13005]	199
[13692]	200	%results
	201	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
	202	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
	203	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
	204	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
[18578]	205	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[18506]	206	if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
[18578]	207	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
	208	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
	209	if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
[15021]	210	%gia
	211	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
	212	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
	213
[13692]	214	%elementstype
	215	if ~isnan(md.flowequation.element_equation)
	216	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
	217	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]	218	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
	219	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
	220	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]	221	end
[13005]	222
[13692]	223	%boundary conditions
[15771]	224	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
	225	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
	226	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
	227	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
	228	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[15767]	229	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
[17991]	230	if ~isnan(md.damage.spcdamage), md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
[13692]	231	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]	232
[18506]	233	% Hydrologydc variables
	234	if isa(md.hydrology,'hydrologydc');
	235	md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
	236	md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
	237	md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
	238	md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
	239	if(md.hydrology.isefficientlayer==1)
	240	md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
	241	end
	242	end
	243
[13692]	244	%materials
	245	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
	246	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]	247
	248	%damage:
[17940]	249	if md.damage.isdamage,
	250	md.damage.D=DepthAverage(md,md.damage.D);
	251	end
[13005]	252
[13692]	253	%special for thermal modeling:
[18378]	254	if ~isnan(md.basalforcings.groundedice_melting_rate),
	255	md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
	256	end
	257	if ~isnan(md.basalforcings.floatingice_melting_rate),
	258	md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
	259	end
[13692]	260	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]	261
[13692]	262	%update of connectivity matrix
	263	md.mesh.average_vertex_connectivity=25;
[13005]	264
[13692]	265	%Collapse the mesh
	266	nodes2d=md.mesh.numberofvertices2d;
	267	elements2d=md.mesh.numberofelements2d;
[13005]	268
[13692]	269	%parameters
	270	md.geometry.surface=project2d(md,md.geometry.surface,1);
	271	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
[17590]	272	md.geometry.base=project2d(md,md.geometry.base,1);
[18480]	273	if ~isnan(md.geometry.bed),
	274	md.geometry.bed=project2d(md,md.geometry.bed,1);
	275	end
[17991]	276
[18378]	277	if ~isnan(md.mask.groundedice_levelset),
	278	md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
	279	end
	280	if ~isnan(md.mask.ice_levelset),
	281	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
	282	end
[13005]	283
[13692]	284	%lat long
	285	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
	286	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
[13005]	287
[13692]	288	%Initialize with the 2d mesh
[17724]	289	mesh=mesh2d();
	290	mesh.x=md.mesh.x2d;
	291	mesh.y=md.mesh.y2d;
	292	mesh.numberofvertices=md.mesh.numberofvertices2d;
	293	mesh.numberofelements=md.mesh.numberofelements2d;
	294	mesh.elements=md.mesh.elements2d;
[17991]	295	if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
	296	if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
[17724]	297	md.mesh=mesh;
[18738]	298	md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
	299	md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
	300	md.mesh.segments=contourenvelope(md);
[13005]	301
[13692]	302	end % }}}
	303	function md2 = extract(md,area) % {{{
	304	%extract - extract a model according to an Argus contour or flag list
	305	%
	306	% This routine extracts a submodel from a bigger model with respect to a given contour
	307	% md must be followed by the corresponding exp file or flags list
	308	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
	309	% If user wants every element outside the domain to be
[15564]	310	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]	311	% an empty string '' will be considered as an empty domain
	312	% a string 'all' will be considered as the entire domain
	313	%
	314	% Usage:
	315	% md2=extract(md,area);
	316	%
	317	% Examples:
	318	% md2=extract(md,'Domain.exp');
	319	%
	320	% See also: EXTRUDE, COLLAPSE
[13005]	321
[13692]	322	%copy model
	323	md1=md;
[13005]	324
[13692]	325	%some checks
	326	if ((nargin~=2) \| (nargout~=1)),
	327	help extract
	328	error('extract error message: bad usage');
	329	end
[13005]	330
[13692]	331	%get elements that are inside area
	332	flag_elem=FlagElements(md1,area);
	333	if ~any(flag_elem),
	334	error('extracted model is empty');
	335	end
[13005]	336
[13692]	337	%kick out all elements with 3 dirichlets
	338	spc_elem=find(~flag_elem);
	339	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
	340	flag=ones(md1.mesh.numberofvertices,1);
	341	flag(spc_node)=0;
	342	pos=find(sum(flag(md1.mesh.elements),2)==0);
	343	flag_elem(pos)=0;
[13005]	344
[13692]	345	%extracted elements and nodes lists
	346	pos_elem=find(flag_elem);
	347	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]	348
[13692]	349	%keep track of some fields
	350	numberofvertices1=md1.mesh.numberofvertices;
	351	numberofelements1=md1.mesh.numberofelements;
	352	numberofvertices2=length(pos_node);
	353	numberofelements2=length(pos_elem);
	354	flag_node=zeros(numberofvertices1,1);
	355	flag_node(pos_node)=1;
[13005]	356
[13692]	357	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
	358	Pelem=zeros(numberofelements1,1);
	359	Pelem(pos_elem)=[1:numberofelements2]';
	360	Pnode=zeros(numberofvertices1,1);
	361	Pnode(pos_node)=[1:numberofvertices2]';
[13005]	362
[13857]	363	%renumber the elements (some nodes won't exist anymore)
[13692]	364	elements_1=md1.mesh.elements;
	365	elements_2=elements_1(pos_elem,:);
	366	elements_2(:,1)=Pnode(elements_2(:,1));
	367	elements_2(:,2)=Pnode(elements_2(:,2));
	368	elements_2(:,3)=Pnode(elements_2(:,3));
[17558]	369	if isa(md1.mesh,'mesh3dprisms'),
[13692]	370	elements_2(:,4)=Pnode(elements_2(:,4));
	371	elements_2(:,5)=Pnode(elements_2(:,5));
	372	elements_2(:,6)=Pnode(elements_2(:,6));
	373	end
[13005]	374
[13857]	375	%OK, now create the new model!
[13005]	376
[13857]	377	%take every field from model
[13692]	378	md2=md1;
[13005]	379
[13692]	380	%automatically modify fields
[13005]	381
[13692]	382	%loop over model fields
	383	model_fields=fields(md1);
	384	for i=1:length(model_fields),
	385	%get field
	386	field=md1.(model_fields{i});
	387	fieldsize=size(field);
	388	if isobject(field), %recursive call
	389	object_fields=fields(md1.(model_fields{i}));
	390	for j=1:length(object_fields),
	391	%get field
	392	field=md1.(model_fields{i}).(object_fields{j});
	393	fieldsize=size(field);
	394	%size = number of nodes * n
	395	if fieldsize(1)==numberofvertices1
	396	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
	397	elseif (fieldsize(1)==numberofvertices1+1)
	398	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]	399	%size = number of elements * n
[13692]	400	elseif fieldsize(1)==numberofelements1
	401	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
	402	end
	403	end
	404	else
	405	%size = number of nodes * n
	406	if fieldsize(1)==numberofvertices1
	407	md2.(model_fields{i})=field(pos_node,:);
	408	elseif (fieldsize(1)==numberofvertices1+1)
	409	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]	410	%size = number of elements * n
[13692]	411	elseif fieldsize(1)==numberofelements1
	412	md2.(model_fields{i})=field(pos_elem,:);
	413	end
	414	end
	415	end
[13005]	416
[13692]	417	%modify some specific fields
[13005]	418
[13692]	419	%Mesh
	420	md2.mesh.numberofelements=numberofelements2;
	421	md2.mesh.numberofvertices=numberofvertices2;
	422	md2.mesh.elements=elements_2;
[13005]	423
[13692]	424	%mesh.uppervertex mesh.lowervertex
[17558]	425	if isa(md1.mesh,'mesh3dprisms'),
[13692]	426	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
	427	pos=find(~isnan(md2.mesh.uppervertex));
	428	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]	429
[13692]	430	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
	431	pos=find(~isnan(md2.mesh.lowervertex));
	432	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]	433
[13692]	434	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
	435	pos=find(~isnan(md2.mesh.upperelements));
	436	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]	437
[13692]	438	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
	439	pos=find(~isnan(md2.mesh.lowerelements));
	440	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
	441	end
[13005]	442
[13692]	443	%Initial 2d mesh
[17558]	444	if isa(md1.mesh,'mesh3dprisms'),
[13692]	445	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
	446	pos_elem_2d=find(flag_elem_2d);
	447	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
	448	pos_node_2d=find(flag_node_2d);
[13005]	449
[13692]	450	md2.mesh.numberofelements2d=length(pos_elem_2d);
	451	md2.mesh.numberofvertices2d=length(pos_node_2d);
	452	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
	453	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
	454	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
	455	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]	456
[13692]	457	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
	458	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
	459	end
[13005]	460
[13692]	461	%Edges
[17686]	462	if(dimension(md.mesh)==2),
[17563]	463	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
	464	%renumber first two columns
	465	pos=find(md2.mesh.edges(:,4)~=-1);
	466	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
	467	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
	468	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
	469	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
	470	%remove edges when the 2 vertices are not in the domain.
	471	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
	472	%Replace all zeros by -1 in the last two columns
	473	pos=find(md2.mesh.edges(:,3)==0);
	474	md2.mesh.edges(pos,3)=-1;
	475	pos=find(md2.mesh.edges(:,4)==0);
	476	md2.mesh.edges(pos,4)=-1;
	477	%Invert -1 on the third column with last column (Also invert first two columns!!)
	478	pos=find(md2.mesh.edges(:,3)==-1);
	479	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
	480	md2.mesh.edges(pos,4)=-1;
	481	values=md2.mesh.edges(pos,2);
	482	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
	483	md2.mesh.edges(pos,1)=values;
	484	%Finally remove edges that do not belong to any element
	485	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
	486	md2.mesh.edges(pos,:)=[];
	487	end
[13692]	488	end
[13005]	489
[13692]	490	%Penalties
[15771]	491	if ~isnan(md2.stressbalance.vertex_pairing),
	492	for i=1:size(md1.stressbalance.vertex_pairing,1);
	493	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]	494	end
[15771]	495	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]	496	end
[15767]	497	if ~isnan(md2.masstransport.vertex_pairing),
	498	for i=1:size(md1.masstransport.vertex_pairing,1);
	499	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]	500	end
[15767]	501	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]	502	end
[13005]	503
[13692]	504	%recreate segments
[17558]	505	if isa(md1.mesh,'mesh2d'),
[13692]	506	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	507	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	508	md2.mesh.segments=contourenvelope(md2);
	509	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
	510	else
	511	%First do the connectivity for the contourenvelope in 2d
	512	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
	513	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
[17565]	514	segments=contourenvelope(md2);
	515	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
[13692]	516	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
	517	%Then do it for 3d as usual
	518	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	519	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	520	end
[13005]	521
[13692]	522	%Boundary conditions: Dirichlets on new boundary
	523	%Catch the elements that have not been extracted
	524	orphans_elem=find(~flag_elem);
	525	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
	526	%Figure out which node are on the boundary between md2 and md1
	527	nodestoflag1=intersect(orphans_node,pos_node);
	528	nodestoflag2=Pnode(nodestoflag1);
[15771]	529	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
[13692]	530	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]	531	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
	532	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]	533	else
[15771]	534	md2.stressbalance.spcvx(nodestoflag2)=NaN;
	535	md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]	536	disp(' ')
	537	disp('!! extract warning: spc values should be checked !!')
	538	disp(' ')
	539	end
	540	%put 0 for vz
[15771]	541	md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]	542	end
	543	if ~isnan(md1.thermal.spctemperature),
	544	md2.thermal.spctemperature(nodestoflag2,1)=1;
	545	end
[13005]	546
[13692]	547	%Results fields
	548	if isstruct(md1.results),
	549	md2.results=struct();
	550	solutionfields=fields(md1.results);
	551	for i=1:length(solutionfields),
[14230]	552	if isstruct(md1.results.(solutionfields{i}))
	553	%get subfields
	554	solutionsubfields=fields(md1.results.(solutionfields{i}));
	555	for j=1:length(solutionsubfields),
	556	field=md1.results.(solutionfields{i}).(solutionsubfields{j});
	557	if length(field)==numberofvertices1,
	558	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
	559	elseif length(field)==numberofelements1,
	560	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
	561	else
	562	md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
	563	end
	564	end
	565	else
	566	field=md1.results.(solutionfields{i});
[13692]	567	if length(field)==numberofvertices1,
[14230]	568	md2.results.(solutionfields{i})=field(pos_node);
[13692]	569	elseif length(field)==numberofelements1,
[14230]	570	md2.results.(solutionfields{i})=field(pos_elem);
[13692]	571	else
[14230]	572	md2.results.(solutionfields{i})=field;
[13692]	573	end
	574	end
	575	end
	576	end
[13005]	577
[13692]	578	%Keep track of pos_node and pos_elem
	579	md2.mesh.extractedvertices=pos_node;
	580	md2.mesh.extractedelements=pos_elem;
	581	end % }}}
	582	function md = extrude(md,varargin) % {{{
	583	%EXTRUDE - vertically extrude a 2d mesh
	584	%
	585	% vertically extrude a 2d mesh and create corresponding 3d mesh.
	586	% The vertical distribution can:
	587	% - follow a polynomial law
	588	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
	589	% - be discribed by a list of coefficients (between 0 and 1)
	590	%
	591	%
	592	% Usage:
	593	% md=extrude(md,numlayers,extrusionexponent);
	594	% md=extrude(md,numlayers,lowerexponent,upperexponent);
	595	% md=extrude(md,listofcoefficients);
	596	%
	597	% Example:
[18216]	598	% md=extrude(md,15,1.3);
	599	% md=extrude(md,15,1.3,1.2);
[13692]	600	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
	601	%
	602	% See also: MODELEXTRACT, COLLAPSE
[13005]	603
[13692]	604	%some checks on list of arguments
	605	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
	606	help extrude;
	607	error('extrude error message');
	608	end
[13005]	609
[13692]	610	%Extrude the mesh
	611	if nargin==2, %list of coefficients
	612	clist=varargin{1};
	613	if any(clist<0) \| any(clist>1),
	614	error('extrusioncoefficients must be between 0 and 1');
	615	end
	616	extrusionlist=sort(unique([clist(:);0;1]));
	617	numlayers=length(extrusionlist);
	618	elseif nargin==3, %one polynomial law
	619	if varargin{2}<=0,
	620	help extrude;
	621	error('extrusionexponent must be >=0');
	622	end
	623	numlayers=varargin{1};
	624	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
	625	elseif nargin==4, %two polynomial laws
	626	numlayers=varargin{1};
	627	lowerexp=varargin{2};
	628	upperexp=varargin{3};
[13005]	629
[13692]	630	if varargin{2}<=0 \| varargin{3}<=0,
	631	help extrude;
	632	error('lower and upper extrusionexponents must be >=0');
	633	end
[13005]	634
[13692]	635	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
	636	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
	637	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]	638
[13692]	639	end
[13005]	640
[13692]	641	if numlayers<2,
	642	error('number of layers should be at least 2');
	643	end
[17686]	644	if strcmp(md.mesh.domaintype(),'3D')
[13692]	645	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
	646	end
[13005]	647
[13692]	648	%Initialize with the 2d mesh
[17558]	649	mesh2d = md.mesh;
	650	md.mesh=mesh3dprisms();
	651	md.mesh.x = mesh2d.x;
	652	md.mesh.y = mesh2d.y;
	653	md.mesh.elements = mesh2d.elements;
	654	md.mesh.numberofelements = mesh2d.numberofelements;
	655	md.mesh.numberofvertices = mesh2d.numberofvertices;
	656
	657	md.mesh.lat = mesh2d.lat;
	658	md.mesh.long = mesh2d.long;
[18558]	659	md.mesh.epsg = mesh2d.epsg;
[17558]	660
	661	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
	662	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
	663	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
	664	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
	665
	666	md.mesh.extractedvertices = mesh2d.extractedvertices;
	667	md.mesh.extractedelements = mesh2d.extractedelements;
	668
[13692]	669	x3d=[];
	670	y3d=[];
	671	z3d=[]; %the lower node is on the bed
	672	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
[17590]	673	bed3d=md.geometry.base;
[13005]	674
[13692]	675	%Create the new layers
	676	for i=1:numlayers,
	677	x3d=[x3d; md.mesh.x];
	678	y3d=[y3d; md.mesh.y];
	679	%nodes are distributed between bed and surface accordingly to the given exponent
	680	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
	681	end
	682	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	683
[13692]	684	%Extrude elements
	685	elements3d=[];
	686	for i=1:numlayers-1,
	687	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
	688	end
	689	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	690
[13692]	691	%Keep a trace of lower and upper nodes
[17590]	692	lowervertex=NaN*ones(number_nodes3d,1);
	693	uppervertex=NaN*ones(number_nodes3d,1);
	694	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
	695	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
	696	md.mesh.lowervertex=lowervertex;
	697	md.mesh.uppervertex=uppervertex;
[13005]	698
[13692]	699	%same for lower and upper elements
[17590]	700	lowerelements=NaN*ones(number_el3d,1);
	701	upperelements=NaN*ones(number_el3d,1);
	702	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
	703	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
	704	md.mesh.lowerelements=lowerelements;
	705	md.mesh.upperelements=upperelements;
[13005]	706
[13692]	707	%Save old mesh
	708	md.mesh.x2d=md.mesh.x;
	709	md.mesh.y2d=md.mesh.y;
	710	md.mesh.elements2d=md.mesh.elements;
	711	md.mesh.numberofelements2d=md.mesh.numberofelements;
	712	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]	713
[13692]	714	%Build global 3d mesh
	715	md.mesh.elements=elements3d;
	716	md.mesh.x=x3d;
	717	md.mesh.y=y3d;
	718	md.mesh.z=z3d;
	719	md.mesh.numberofelements=number_el3d;
	720	md.mesh.numberofvertices=number_nodes3d;
	721	md.mesh.numberoflayers=numlayers;
[13005]	722
[13692]	723	%Ok, now deal with the other fields from the 2d mesh:
[13005]	724
[19048]	725	%bedinfo and surface info
	726	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
	727	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
	728	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
	729
[13692]	730	%lat long
	731	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
	732	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[13005]	733
[19048]	734	md.geometry=extrude(md.geometry,md);
	735	md.friction = extrude(md.friction,md);
	736	md.inversion = extrude(md.inversion,md);
[19527]	737	md.smb = extrude(md.smb,md);
[19048]	738	md.initialization = extrude(md.initialization,md);
[13005]	739
[19050]	740	md.flowequation=md.flowequation.extrude(md);
[19048]	741	md.stressbalance=extrude(md.stressbalance,md);
[19050]	742	md.thermal=md.thermal.extrude(md);
	743	md.masstransport=md.masstransport.extrude(md);
[19048]	744	md.calving=extrude(md.calving,md);
	745	md.hydrology = extrude(md.hydrology,md);
[13005]	746
[13692]	747	%connectivity
[17991]	748	if ~isnan(md.mesh.elementconnectivity)
	749	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
	750	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
	751	for i=2:numlayers-1,
	752	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
	753	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
	754	end
	755	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13692]	756	end
[13005]	757
[19048]	758	md.materials=extrude(md.materials,md);
	759	md.damage=extrude(md.damage,md);
	760	md.mask=extrude(md.mask,md);
	761	md.qmu=extrude(md.qmu,md);
	762	md.basalforcings=extrude(md.basalforcings,md);
[13005]	763
[13692]	764	%increase connectivity if less than 25:
	765	if md.mesh.average_vertex_connectivity<=25,
	766	md.mesh.average_vertex_connectivity=100;
	767	end
[13005]	768	end % }}}
[13692]	769	function md = structtomodel(md,structmd) % {{{
[8952]	770
[13692]	771	if ~isstruct(structmd) error('input model is not a structure'); end
[8952]	772
[13692]	773	%loaded model is a struct, initialize output and recover all fields
	774	md = structtoobj(model,structmd);
[8952]	775
[13692]	776	%Old field now classes
	777	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
	778	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]	779
[13692]	780	%Field name change
	781	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	782	if isfield(structmd,'p'), md.friction.p=structmd.p; end
	783	if isfield(structmd,'q'), md.friction.q=structmd.p; end
[18378]	784	if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
[18068]	785	if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
[18378]	786	if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
[19527]	787	if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
[13692]	788	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
	789	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
	790	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
	791	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
[17610]	792	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
[13692]	793	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
	794	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
	795	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]	796	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]	797	if isfield(structmd,'g'), md.constants.g=structmd.g; end
	798	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
[19527]	799	if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
[18068]	800	if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
[13692]	801	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
	802	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	803	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
	804	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
	805	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
	806	if isfield(structmd,'riftproperties'), %old implementation
	807	md.rifts=rifts();
	808	md.rifts.riftproperties=structmd.riftproperties;
	809	md.rifts.riftstruct=structmd.rifts;
	810	md.rifts.riftproperties=structmd.riftinfo;
	811	end
	812	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
	813	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
	814	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
	815	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
	816	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
	817	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
	818	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
	819	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
	820	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
	821	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
	822	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
	823	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
	824	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
	825	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
	826	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
	827	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
	828	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
	829	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
	830	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
	831	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
	832	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
	833	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]	834	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
	835	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
	836	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
	837	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
	838	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]	839	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
	840	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
	841	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
	842	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]	843	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]	844	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
	845	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
	846	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]	847	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
	848	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]	849	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
	850	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
	851	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
	852	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]	853	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]	854	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]	855	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
	856	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
	857	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
	858	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
	859	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
	860	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
	861	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
	862	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
	863	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
	864	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
	865	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
	866	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
	867	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
	868	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
	869	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
	870	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
	871	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
	872	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
	873	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
	874	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
[17590]	875	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
[13692]	876	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
[17590]	877	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
[13692]	878	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
	879	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
	880	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
	881	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
	882	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
	883	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
	884	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
	885	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
	886	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
	887	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
	888	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
	889	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
	890	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
	891	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
	892	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
	893	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
	894	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
	895	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
	896	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
	897	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
	898	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
	899	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
	900	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
[17610]	901	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
[13692]	902	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
	903	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
	904	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
	905	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]	906	if isfield(structmd,'edges'),
	907	md.mesh.edges=structmd.edges;
	908	md.mesh.edges(isnan(md.mesh.edges))=-1;
	909	end
[13692]	910	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
	911	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
	912	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
	913	if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
[15771]	914	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]	915	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
	916	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]	917
[13692]	918	if isnumeric(md.verbose),
	919	md.verbose=verbose;
	920	end
[15768]	921
[13692]	922	if isfield(structmd,'spcvelocity'),
[15771]	923	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	924	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	925	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	926	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
	927	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
	928	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]	929	end
	930	if isfield(structmd,'spcvx'),
[15771]	931	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	932	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]	933	end
	934	if isfield(structmd,'spcvy'),
[15771]	935	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	936	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]	937	end
	938	if isfield(structmd,'spcvz'),
[15771]	939	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	940	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]	941	end
[14620]	942	if isfield(structmd,'pressureload'),
	943	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]	944	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
	945	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
	946	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]	947	end
[13692]	948	end
	949	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
	950	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
	951	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
	952	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
	953	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
	954	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
	955	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
	956	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
	957	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
	958	end
	959	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
	960	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
	961	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
	962	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
	963	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
	964	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
	965	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
	966	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
	967	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
	968	end
	969	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
	970	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
	971	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
	972	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
	973	end
	974	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
	975	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
[17941]	976	if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
[13692]	977	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
	978	end
	979	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
	980	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
	981	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
	982	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
	983	end
	984	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
	985	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
	986	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
	987	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
	988	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
	989	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
	990	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
	991	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
	992	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
	993	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
	994	end
[11659]	995
[13692]	996	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
	997	md.thermal.stabilization=2;
[15767]	998	md.masstransport.stabilization=1;
[13692]	999	md.balancethickness.stabilization=1;
	1000	end
[15767]	1001	if isnumeric(md.masstransport.hydrostatic_adjustment)
	1002	if md.masstransport.hydrostatic_adjustment==269,
	1003	md.masstransport.hydrostatic_adjustment='Incremental';
[13692]	1004	else
[15767]	1005	md.masstransport.hydrostatic_adjustment='Absolute';
[13692]	1006	end
	1007	end
[8952]	1008
[13692]	1009	%New fields
[19124]	1010	if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1011	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
	1012	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
	1013	end
[19124]	1014	if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1015	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
	1016	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
	1017	end
	1018	if ~isfield(structmd,'diagnostic_ref');
[15771]	1019	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]	1020	end
[14529]	1021	if ~isfield(structmd,'loadingforce');
[15771]	1022	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]	1023	end
[15768]	1024
	1025	%2013 August 9
	1026	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
	1027	disp('Recovering old prognostic class');
	1028	md.masstransport=masstransport(structmd.prognostic);
	1029	end
[15771]	1030	%2013 August 9
[15775]	1031	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
[15771]	1032	disp('Recovering old diagnostic class');
[15775]	1033	md.stressbalance=stressbalance(structmd.diagnostic);
[15771]	1034	end
[19642]	1035	%2014 January 9th
	1036	if isfield(structmd,'surfaceforcings'),
	1037	disp('Recovering old surfaceforcings class');
	1038	mass_balance=structmd.surfaceforcings.mass_balance;
	1039	md.smb=SMB();
	1040	md.smb.mass_balance=mass_balance;
	1041	end
	1042	%2015 September 10
	1043	if isfield(structmd,'surfaceforcings') & isa(md.smb,'SMB'),
	1044	disp('Recovering old SMB class');
	1045	md.smb=SMBforcing(structmd.surfaceforcings);
	1046	end
	1047
[13692]	1048	end% }}}
	1049	function md = setdefaultparameters(md) % {{{
[8926]	1050
[13692]	1051	%initialize subclasses
[17558]	1052	md.mesh = mesh2d();
[13692]	1053	md.mask = mask();
	1054	md.constants = constants();
	1055	md.geometry = geometry();
	1056	md.initialization = initialization();
[19527]	1057	md.smb = SMBforcing();
[13692]	1058	md.basalforcings = basalforcings();
	1059	md.friction = friction();
	1060	md.rifts = rifts();
	1061	md.timestepping = timestepping();
	1062	md.groundingline = groundingline();
	1063	md.materials = matice();
[16160]	1064	md.damage = damage();
[13692]	1065	md.flowequation = flowequation();
	1066	md.debug = debug();
[14558]	1067	md.verbose = verbose();
[13692]	1068	md.settings = settings();
[17932]	1069	md.toolkits = toolkits();
[13692]	1070	md.cluster = generic();
	1071	md.balancethickness = balancethickness();
[17079]	1072	md.stressbalance = stressbalance();
[14555]	1073	md.hydrology = hydrologyshreve();
[17079]	1074	md.masstransport = masstransport();
[13692]	1075	md.thermal = thermal();
	1076	md.steadystate = steadystate();
	1077	md.transient = transient();
[18757]	1078	md.calving = calving();
[14724]	1079	md.gia = gia();
[13692]	1080	md.autodiff = autodiff();
	1081	md.flaim = flaim();
	1082	md.inversion = inversion();
	1083	md.qmu = qmu();
	1084	md.radaroverlay = radaroverlay();
	1085	md.results = struct();
[16388]	1086	md.outputdefinition = outputdefinition();
[13692]	1087	md.miscellaneous = miscellaneous();
	1088	md.private = private();
	1089	end
	1090	%}}}
[17483]	1091	function md = tetras(md,varargin) % {{{
	1092	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
	1093	%
	1094	% Usage:
	1095	% md=tetra(md)
	1096
	1097	if ~isa(md.mesh,'mesh3dprisms')
	1098	error('mesh is not a 3d prismatic mesh');
	1099	end
	1100
	1101	%Initialize tetra mesh
	1102	md.mesh=mesh3dtetras(md.mesh);
	1103
[17754]	1104	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
	1105	steiner = 0;
	1106	nbv = md.mesh.numberofvertices;
	1107	nbt = 3*md.mesh.numberofelements;
	1108	elements = zeros(nbt,4);
	1109	for i=1:md.mesh.numberofelements
	1110	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
	1111	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
	1112	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1113	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1114	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1115	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1116	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1117	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1118	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
	1119	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
	1120	elements(end+1,:) = [v2 v3 v5 v7];
	1121	elements(end+1,:) = [v3 v5 v6 v7];
	1122	elements(end+1,:) = [v1 v3 v6 v7];
	1123	elements(end+1,:) = [v1 v4 v6 v7];
	1124	elements(end+1,:) = [v4 v5 v6 v7];
	1125	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1126	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
	1127	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1128	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1129	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1130	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1131	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
	1132	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1133	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1134	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1135	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1136	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
[18142]	1137	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
[17754]	1138	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1139	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1140	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
	1141	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1142	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1143	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
	1144	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1145	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1146	elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
	1147	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1148	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1149	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1150	elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
	1151	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1152	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
	1153	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1154	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1155	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1156	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1157	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1158	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1159	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
	1160	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
	1161	elements(end+1,:) = [v2 v5 v6 v7];
	1162	elements(end+1,:) = [v2 v3 v6 v7];
	1163	elements(end+1,:) = [v3 v4 v6 v7];
	1164	elements(end+1,:) = [v1 v3 v4 v7];
	1165	elements(end+1,:) = [v4 v5 v6 v7];
	1166	else
	1167	error('Case not supported'); %not supposed to happen!
	1168	end
[17774]	1169	%Reorder elements to make sure they are direct
	1170	for j=1:3
	1171	element = elements(3*(i-1)+j,:);
	1172	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
	1173	if det(matrix)>0,
	1174	elements(3*(i-1)+j,1)=element(2);
	1175	elements(3*(i-1)+j,2)=element(1);
	1176	end
	1177	end
[17754]	1178	end
	1179	%%Split in 3 tetras
	1180	%subelement1 = [1 2 3 5];
	1181	%subelement2 = [4 6 5 1];
	1182	%subelement3 = [5 6 3 1];
	1183	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
[17774]	1184	if steiner==0,
	1185	disp('No Steiner point required to split prismatic mesh into tets');
	1186	else
	1187	disp([num2str(steiner) ' Steiner points had to be included'])
	1188	error('Steiner point not supported yet');
	1189	end
[17754]	1190
[17483]	1191	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
	1192
	1193	md.mesh.elements=elements;
	1194	md.mesh.numberofelements=size(elements,1);
	1195
	1196	%p and q (same deal, except for element that are on the bedrock: )
[17774]	1197	if ~isnan(md.friction.p),
	1198	md.friction.p=md.friction.p(pos_elements);
	1199	md.friction.q=md.friction.q(pos_elements);
	1200	end
[17483]	1201
	1202	%elementstype
	1203	if ~isnan(md.flowequation.element_equation)
	1204	oldelements_type=md.flowequation.element_equation;
	1205	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
	1206	end
	1207
	1208	%connectivity
	1209	md.mesh.elementconnectivity=NaN;
	1210
	1211	%materials
[17774]	1212	if ~isnan(md.materials.rheology_n),
	1213	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
	1214	end
[17483]	1215
	1216	%increase connectivity if less than 25:
	1217	if md.mesh.average_vertex_connectivity<=25,
	1218	md.mesh.average_vertex_connectivity=100;
	1219	end
	1220	end % }}}
[19040]	1221	function disp(self) % {{{
	1222	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
	1223	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
	1224	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
	1225	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
[19527]	1226	disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
[19040]	1227	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
	1228	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
	1229	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
	1230	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
	1231	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
	1232	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
	1233	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
	1234	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
	1235	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
	1236	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
	1237	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
	1238	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
	1239	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
	1240	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
	1241	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
	1242	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
	1243	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
	1244	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
	1245	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
	1246	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
	1247	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
	1248	disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
	1249	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
	1250	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
	1251	disp(sprintf('%19s: %-22s -- %s','flaim' ,['[1x1 ' class(self.flaim) ']'],'flaim parameters'));
	1252	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
	1253	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
	1254	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
	1255	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
	1256	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
	1257	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
[13692]	1258	end % }}}
[19040]	1259	function memory(self) % {{{
[15106]	1260
[14611]	1261	disp(sprintf('\nMemory imprint:\n'));
[14307]	1262
[14603]	1263	fields=properties('model');
	1264	mem=0;
[15106]	1265
[14603]	1266	for i=1:length(fields),
[19040]	1267	field=self.(fields{i});
[14603]	1268	s=whos('field');
	1269	mem=mem+s.bytes/1e6;
[14611]	1270	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]	1271	end
[14603]	1272	disp(sprintf('%19s--%10s','--------------','--------------'));
	1273	disp(sprintf('%19s: %g Mb','Total',mem));
[14307]	1274	end % }}}
[19040]	1275	function netcdf(self,filename) % {{{
[14603]	1276	%NETCDF - save model as netcdf
	1277	%
	1278	% Usage:
	1279	% netcdf(md,filename)
	1280	%
	1281	% Example:
	1282	% netcdf(md,'model.nc');
	1283
	1284	disp('Saving model as NetCDF');
	1285	%1. Create NetCDF file
	1286	ncid=netcdf.create(filename,'CLOBBER');
	1287	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[19040]	1288	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
[14603]	1289	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
	1290	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
	1291
[14611]	1292	%Preallocate variable id, needed to write variables in netcdf file
[14631]	1293	var_id=zeros(1000,1);%preallocate
[14609]	1294
	1295	for step=1:2,
	1296	counter=0;
[19040]	1297	[var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
[14609]	1298	if step==1, netcdf.endDef(ncid); end
[14603]	1299	end
[14611]	1300
[14631]	1301	if counter>1000,
	1302	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]	1303	end
	1304
	1305	netcdf.close(ncid)
[14603]	1306	end % }}}
[19040]	1307	function xylim(self) % {{{
[14405]	1308
[19040]	1309	xlim([min(self.mesh.x) max(self.mesh.x)]);
	1310	ylim([min(self.mesh.y) max(self.mesh.y)])
[14405]	1311	end % }}}
[15316]	1312	function md=upload(md) % {{{
	1313	%the goal of this routine is to upload the model onto a server, and to empty it.
	1314	%So first, save the model with a unique name and upload the file to the server:
	1315	random_part=fix(rand(1)*10000);
	1316	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
	1317	eval(['save ' id ' md']);
	1318
	1319	%Now, upload the file:
	1320	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
	1321
	1322	%Now, empty this model of everything except settings, and record name of file we just uploaded!
	1323	settings_back=md.settings;
	1324	md=model();
	1325	md.settings=settings_back;
	1326	md.settings.upload_filename=id;
	1327
	1328	%get locally rid of file that was uploaded
	1329	eval(['delete ' id]);
	1330
	1331	end % }}}
	1332	function md=download(md) % {{{
[15643]	1333
[15316]	1334	%the goal of this routine is to download the internals of the current model from a server, because
	1335	%this model is empty, except for the settings which tell us where to go and find this model!
[15643]	1336
[15316]	1337	%Download the file:
	1338	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
	1339
	1340	name=md.settings.upload_filename;
	1341
	1342	%Now, load this model:
	1343	md=loadmodel(md.settings.upload_filename);
	1344
	1345	%get locally rid of file that was downloaded
	1346	eval(['delete ' name]);
	1347
	1348	end % }}}
[13692]	1349	end
[8926]	1350	end

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