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source: issm/trunk-jpl/src/m/classes/model.m@ 26209

Last change on this file since 26209 was 26209, checked in by schlegel, 4 years ago
BUG: isclimatology not transferring correctly to cycle_forcing from SMB in old models
File size: 76.5 KB

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1	%MODEL class definition
2	%
3	% Usage:
4	% md = model(varargin)
5
6	classdef model
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;
12
13	geometry = 0;
14	constants = 0;
15	smb = 0;
16	basalforcings = 0;
17	materials = 0;
18	damage = 0;
19	friction = 0;
20	flowequation = 0;
21	timestepping = 0;
22	initialization = 0;
23	rifts = 0;
24	dsl = 0;
25	solidearth = 0;
26
27	debug = 0;
28	verbose = 0;
29	settings = 0;
30	toolkits = 0;
31	cluster = 0;
32
33	balancethickness = 0;
34	stressbalance = 0;
35	groundingline = 0;
36	hydrology = 0;
37	masstransport = 0;
38	thermal = 0;
39	steadystate = 0;
40	transient = 0;
41	levelset = 0;
42	calving = 0;
43	frontalforcings = 0;
44	love = 0;
45	esa = 0;
46	sampling = 0;
47
48	autodiff = 0;
49	inversion = 0;
50	qmu = 0;
51	amr = 0;
52	results = 0;
53	outputdefinition = 0;
54	radaroverlay = 0;
55	miscellaneous = 0;
56	private = 0;
57
58	%}}}
59	end
60	methods (Static)
61	function md = loadobj(md) % {{{
62	% This function is directly called by matlab when a model object is
63	% loaded. If the input is a struct it is an old version of model and
64	% old fields must be recovered (make sure they are in the deprecated
65	% model properties)
66
67	if verLessThan('matlab','7.9'),
68	disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
69	disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
70
71	% This is a Matlab bug: all the fields of md have their default value
72	% Example of error message:
73	% Warning: Error loading an object of class 'model':
74	% Undefined function or method 'exist' for input arguments of type 'cell'
75	%
76	% This has been fixed in MATLAB 7.9 (R2009b) and later versions
77	end
78
79	if isstruct(md)
80	disp('Recovering model object from a previous version');
81	md = structtomodel(model,md);
82	end
83
84	%2012 August 4th
85	if isa(md.materials,'materials'),
86	disp('Recovering old materials');
87	if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
88	md.materials=matice(md.materials);
89	else
90	md.materials=matdamageice(md.materials);
91	end
92	end
93	%2013 April 12
94	if numel(md.stressbalance.loadingforce==1)
95	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
96	end
97	%2013 April 17
98	if isa(md.hydrology,'hydrology'),
99	disp('Recovering old hydrology class');
100	md.hydrology=hydrologyshreve(md.materials);
101	end
102	%2013 October 9
103	if ~isa(md.damage,'damage'),
104	md.damage=damage();
105	md.damage.D=zeros(md.mesh.numberofvertices,1);
106	md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
107	end
108	%2013 November 18
109	if ~isa(md.outputdefinition,'outputdefinition'),
110	md.outputdefinition=outputdefinition();
111	end
112	%2014 March 26th
113	if isa(md.mesh,'mesh'),
114	disp('Recovering old mesh class');
115	if isprop(md.mesh,'dimension'),
116	if md.mesh.dimension==2,
117	md.mesh=mesh2d(md.mesh);
118	else
119	md.mesh=mesh3dprisms(md.mesh);
120	end
121	else
122	md.mesh=mesh2dvertical(md.mesh);
123	end
124	end
125	%2014 November 12
126	if isa(md.calving,'double'); md.calving=calving(); end
127	%2016 October 11
128	if isa(md.esa,'double'); md.esa=esa(); end
129	%2017 February 10th
130	if isa(md.settings,'settings'), %this 'isa' verification: 2018 October 24th
131	if md.settings.solver_residue_threshold==0,
132	md.settings.solver_residue_threshold = 1e-6;
133	end
134	end
135	%2017 May 4th
136	if isa(md.amr,'double'); md.amr=amr(); end
137	%2017 Aug 29th
138	if isa(md.love,'double'); md.love=fourierlove(); end
139	%2017 Oct 26th
140	if isa(md.calving,'calvingdev')
141	disp('Warning: calvingdev is now calvingvonmises');
142	md.calving=calvingvonmises(md.calving);
143	end
144	%2017 Dec 21st (needs to be here)
145	if isempty(md.settings)
146	disp('Warning: md.settings had to be reset, make sure to adjust md.settings.output_frequency and other fields');
147	md.settings = issmsettings();
148	end
149	%2018 Dec 1st
150	if md.settings.sb_coupling_frequency==0
151	md.settings.sb_coupling_frequency=1;
152	end
153	%2019 Jan..
154	if isa(md.frontalforcings,'double');
155	if(isprop('meltingrate',md.calving) & ~isnan(md.calving.meltingrate))
156	gia disp('Warning: md.calving.meltingrate is now in md.frontalforcings');
157	end
158	md.frontalforcings=frontalforcings(md.calving);
159	end
160	%2019 Feb 26
161	if isa(md.settings.results_on_nodes,'double')
162	if md.settings.results_on_nodes == 0
163	md.settings.results_on_nodes = {};
164	else
165	md.settings.results_on_nodes = {'all'};
166	end
167	end
168	%2019 Mar 28, updated 2021 April 23
169	if isa(md.smb,'SMBcomponents') \| isa(md.smb,'SMBmeltcomponents') \| isa(md.smb,'SMBforcing') \| isa(md.smb,'SMBgemb')
170	if any(strcmp(fieldnames(md.smb),'isclimatology'))
171	if isa(md.smb.isclimatology,'double')
172	if prod(size(md.smb.isclimatology)) ~= 1
173	md.smb.isclimatology = 0;
174	end
175	md.timestepping.cycle_forcing=md.smb.isclimatology;
176	end
177	end
178	end
179	%2019 Dec 16
180	if isa(md.dsl,'double')
181	md.dsl=dsl();
182	end
183	%2020 April 24
184	if isa(md.smb,'SMBgemb')
185	if isa(md.smb.isconstrainsurfaceT,'double')
186	if prod(size(md.smb.isconstrainsurfaceT)) ~= 1
187	md.smb.isconstrainsurfaceT = 0;
188	end
189	end
190	end
191	%2021 February 17
192	if isa(md.sampling,'double'); md.sampling=sampling(); end
193	end% }}}
194	end
195	methods
196	function md = model(varargin) % {{{
197
198	switch nargin
199	case 0
200	md=setdefaultparameters(md,'earth');
201	otherwise
202	options=pairoptions(varargin{:});
203	planet=getfieldvalue(options,'planet','earth');
204	md=setdefaultparameters(md,planet);
205	end
206
207	end
208	%}}}
209	function md = setdefaultparameters(md,planet) % {{{
210
211	%initialize subclasses
212	md.mesh = mesh2d();
213	md.mask = mask();
214	md.constants = constants();
215	md.geometry = geometry();
216	md.initialization = initialization();
217	md.smb = SMBforcing();
218	md.basalforcings = basalforcings();
219	md.friction = friction();
220	md.rifts = rifts();
221	md.solidearth = solidearth(planet);
222	md.dsl = dsl();
223	md.timestepping = timestepping();
224	md.groundingline = groundingline();
225	md.materials = matice();
226	md.damage = damage();
227	md.flowequation = flowequation();
228	md.debug = debug();
229	md.verbose = verbose();
230	md.settings = issmsettings();
231	md.toolkits = toolkits();
232	md.cluster = generic();
233	md.balancethickness = balancethickness();
234	md.stressbalance = stressbalance();
235	md.hydrology = hydrologyshreve();
236	md.masstransport = masstransport();
237	md.thermal = thermal();
238	md.steadystate = steadystate();
239	md.transient = transient();
240	md.levelset = levelset();
241	md.calving = calving();
242	md.frontalforcings = frontalforcings();
243	md.love = fourierlove();
244	md.esa = esa();
245	md.sampling = sampling();
246	md.autodiff = autodiff();
247	md.inversion = inversion();
248	md.qmu = qmu();
249	md.amr = amr();
250	md.radaroverlay = radaroverlay();
251	md.results = struct();
252	md.outputdefinition = outputdefinition();
253	md.miscellaneous = miscellaneous();
254	md.private = private();
255	end
256	%}}}
257	function md = checkmessage(md,string) % {{{
258	if(nargout~=1) error('wrong usage, model must be an output'); end
259	disp(['model not consistent: ' string]);
260	md.private.isconsistent=false;
261	end
262	%}}}
263	function md = collapse(md)% {{{
264	%COLLAPSE - collapses a 3d mesh into a 2d mesh
265	%
266	% This routine collapses a 3d model into a 2d model
267	% and collapses all the fields of the 3d model by
268	% taking their depth-averaged values
269	%
270	% Usage:
271	% md=collapse(md)
272	%
273	% See also: EXTRUDE, MODELEXTRACT
274
275	%Check that the model is really a 3d model
276	if ~strcmp(md.mesh.elementtype(),'Penta'),
277	error('collapse error message: only 3d mesh can be collapsed')
278	end
279
280	%Start with changing all the fields from the 3d mesh
281
282	%dealing with the friction law
283	%drag is limited to nodes that are on the bedrock.
284	if isa(md.friction,'friction'),
285	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
286	md.friction.p=project2d(md,md.friction.p,1);
287	md.friction.q=project2d(md,md.friction.q,1);
288	elseif isa(md.friction,'frictioncoulomb'),
289	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
290	md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1);
291	md.friction.p=project2d(md,md.friction.p,1);
292	md.friction.q=project2d(md,md.friction.q,1);
293	elseif isa(md.friction,'frictionhydro'),
294	md.friction.q=project2d(md,md.friction.q,1);
295	md.friction.C=project2d(md,md.friction.C,1);
296	md.friction.As=project2d(md,md.friction.As,1);
297	md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
298	elseif isa(md.friction,'frictionwaterlayer'),
299	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
300	md.friction.p=project2d(md,md.friction.p,1);
301	md.friction.q=project2d(md,md.friction.q,1);
302	md.friction.water_layer=project2d(md,md.friction.water_layer,1);
303	elseif isa(md.friction,'frictionweertman'),
304	md.friction.C=project2d(md,md.friction.C,1);
305	md.friction.m=project2d(md,md.friction.m,1);
306	elseif isa(md.friction,'frictionweertmantemp'),
307	md.friction.C=project2d(md,md.friction.C,1);
308	md.friction.m=project2d(md,md.friction.m,1);
309	elseif isa(md.friction,'frictionjosh'),
310	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
311	md.friction.pressure_adjusted_temperature=project2d(md,md.friction.pressure_adjusted_temperature,1);
312	else
313	disp('friction type not supported');
314	end
315
316	%observations
317	if ~isnan(md.inversion.vx_obs),
318	md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers);
319	end
320	if ~isnan(md.inversion.vy_obs),
321	md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers);
322	end
323	if ~isnan(md.inversion.vel_obs),
324	md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers);
325	end
326	if ~isnan(md.inversion.thickness_obs),
327	md.inversion.thickness_obs=project2d(md,md.inversion.thickness_obs,md.mesh.numberoflayers);
328	end
329	if ~isnan(md.inversion.cost_functions_coefficients),
330	md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers);
331	end
332	if numel(md.inversion.min_parameters)>1,
333	md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers);
334	end
335	if numel(md.inversion.max_parameters)>1,
336	md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers);
337	end
338	if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
339	md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
340	elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
341	md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
342	end
343
344	%results
345	if ~isnan(md.initialization.vx),
346	md.initialization.vx=DepthAverage(md,md.initialization.vx);
347	end
348	if ~isnan(md.initialization.vy),
349	md.initialization.vy=DepthAverage(md,md.initialization.vy);
350	end
351	if ~isnan(md.initialization.vz),
352	md.initialization.vz=DepthAverage(md,md.initialization.vz);
353	end
354	if ~isnan(md.initialization.vel),
355	md.initialization.vel=DepthAverage(md,md.initialization.vel);
356	end
357	if ~isnan(md.initialization.temperature),
358	md.initialization.temperature=DepthAverage(md,md.initialization.temperature);
359	end
360	if ~isnan(md.initialization.pressure),
361	md.initialization.pressure=project2d(md,md.initialization.pressure,1);
362	end
363	if ~isnan(md.initialization.sediment_head),
364	md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);
365	end
366	if ~isnan(md.initialization.epl_head),
367	md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);
368	end
369	if ~isnan(md.initialization.epl_thickness),
370	md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);
371	end
372	if ~isnan(md.initialization.waterfraction),
373	md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);
374	end
375	if ~isnan(md.initialization.watercolumn),
376	md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);
377	end
378
379
380	%elementstype
381	if ~isnan(md.flowequation.element_equation)
382	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
383	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
384	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
385	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
386	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
387	end
388
389	%boundary conditions
390	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
391	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
392	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
393	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
394	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
395	if numel(md.masstransport.spcthickness)>1,
396	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
397	end
398	if numel(md.damage.spcdamage)>1,
399	md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers);
400	end
401	if numel(md.levelset.spclevelset)>1,
402	md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers);
403	end
404	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
405
406	% Hydrologydc variables
407	if isa(md.hydrology,'hydrologydc');
408	md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
409	md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
410	md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
411	md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
412	if(md.hydrology.isefficientlayer==1)
413	md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
414	end
415	end
416
417	%materials
418	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
419	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
420
421	%damage:
422	if md.damage.isdamage,
423	md.damage.D=DepthAverage(md,md.damage.D);
424	end
425
426	%special for thermal modeling:
427	if ~isnan(md.basalforcings.groundedice_melting_rate),
428	md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
429	end
430	if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
431	md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
432	end
433	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
434
435	if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
436	md.calving.coeff=project2d(md,md.calving.coeff,1);
437	end
438	if isprop(md.frontalforcings,'meltingrate') & ~isnan(md.frontalforcings.meltingrate),
439	md.frontalforcings.meltingrate=project2d(md,md.frontalforcings.meltingrate,1);
440	end
441
442	%update of connectivity matrix
443	md.mesh.average_vertex_connectivity=25;
444
445	%Collapse the mesh
446	nodes2d=md.mesh.numberofvertices2d;
447	elements2d=md.mesh.numberofelements2d;
448
449	%parameters
450	md.geometry.surface=project2d(md,md.geometry.surface,1);
451	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
452	md.geometry.base=project2d(md,md.geometry.base,1);
453	if ~isnan(md.geometry.bed),
454	md.geometry.bed=project2d(md,md.geometry.bed,1);
455	end
456	if ~isnan(md.mask.ocean_levelset),
457	md.mask.ocean_levelset=project2d(md,md.mask.ocean_levelset,1);
458	end
459	if ~isnan(md.mask.ice_levelset),
460	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
461	end
462
463	%lat long
464	if numel(md.mesh.lat)==md.mesh.numberofvertices,
465	md.mesh.lat=project2d(md,md.mesh.lat,1);
466	end
467	if numel(md.mesh.long)==md.mesh.numberofvertices,
468	md.mesh.long=project2d(md,md.mesh.long,1);
469	end
470
471	%outputdefinitions
472	for i=1:length(md.outputdefinition.definitions)
473	if isobject(md.outputdefinition.definitions{i})
474	%get subfields
475	solutionsubfields=fields(md.outputdefinition.definitions{i});
476	for j=1:length(solutionsubfields),
477	field=md.outputdefinition.definitions{i}.(solutionsubfields{j});
478	if length(field)==md.mesh.numberofvertices \| length(field)==md.mesh.numberofelements,
479	md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1);
480	end
481	end
482	end
483	end
484
485	%Initialize the 2d mesh
486	mesh=mesh2d();
487	mesh.x=md.mesh.x2d;
488	mesh.y=md.mesh.y2d;
489	mesh.numberofvertices=md.mesh.numberofvertices2d;
490	mesh.numberofelements=md.mesh.numberofelements2d;
491	mesh.elements=md.mesh.elements2d;
492	if numel(md.mesh.lat)==md.mesh.numberofvertices,
493	mesh.lat=project2d(md,md.mesh.lat,1);
494	end
495	if numel(md.mesh.long)==md.mesh.numberofvertices,
496	mesh.long=project2d(md,md.mesh.long,1);
497	end
498	mesh.epsg=md.mesh.epsg;
499	if numel(md.mesh.scale_factor)==md.mesh.numberofvertices,
500	mesh.scale_factor=project2d(md,md.mesh.scale_factor,1);
501	end
502	if ~isnan(md.mesh.vertexonboundary),
503	mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
504	end
505	if ~isnan(md.mesh.elementconnectivity),
506	mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
507	end
508	md.mesh=mesh;
509	md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
510	md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
511	md.mesh.segments=contourenvelope(md.mesh);
512
513	end % }}}
514	function md2 = extract(md,area,varargin) % {{{
515	%extract - extract a model according to an Argus contour or flag list
516	%
517	% This routine extracts a submodel from a bigger model with respect to a given contour
518	% md must be followed by the corresponding exp file or flags list
519	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
520	% If user wants every element outside the domain to be
521	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
522	% an empty string '' will be considered as an empty domain
523	% a string 'all' will be considered as the entire domain
524	%
525	% Usage:
526	% md2=extract(md,area);
527	%
528	% Examples:
529	% md2=extract(md,'Domain.exp');
530	%
531	% See also: EXTRUDE, COLLAPSE
532
533	%copy model
534	md1=md;
535
536	%recover optoins:
537	options=pairoptions(varargin{:});
538
539	%some checks
540	if ((nargin<2) \| (nargout~=1)),
541	help extract
542	error('extract error message: bad usage');
543	end
544
545	%get elements that are inside area
546	flag_elem=FlagElements(md1,area);
547	if ~any(flag_elem),
548	error('extracted model is empty');
549	end
550
551	%kick out all elements with 3 dirichlets
552	if getfieldvalue(options,'spccheck',1)
553	spc_elem=find(~flag_elem);
554	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
555	flag=ones(md1.mesh.numberofvertices,1);
556	flag(spc_node)=0;
557	pos=find(sum(flag(md1.mesh.elements),2)==0);
558	flag_elem(pos)=0;
559	end
560
561	%extracted elements and nodes lists
562	pos_elem=find(flag_elem);
563	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
564
565	%keep track of some fields
566	numberofvertices1=md1.mesh.numberofvertices;
567	numberofelements1=md1.mesh.numberofelements;
568	numberofvertices2=length(pos_node);
569	numberofelements2=length(pos_elem);
570	flag_node=zeros(numberofvertices1,1);
571	flag_node(pos_node)=1;
572
573	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
574	Pelem=zeros(numberofelements1,1);
575	Pelem(pos_elem)=[1:numberofelements2]';
576	Pnode=zeros(numberofvertices1,1);
577	Pnode(pos_node)=[1:numberofvertices2]';
578
579	%renumber the elements (some nodes won't exist anymore)
580	elements_1=md1.mesh.elements;
581	elements_2=elements_1(pos_elem,:);
582	elements_2(:,1)=Pnode(elements_2(:,1));
583	elements_2(:,2)=Pnode(elements_2(:,2));
584	elements_2(:,3)=Pnode(elements_2(:,3));
585	if isa(md1.mesh,'mesh3dprisms'),
586	elements_2(:,4)=Pnode(elements_2(:,4));
587	elements_2(:,5)=Pnode(elements_2(:,5));
588	elements_2(:,6)=Pnode(elements_2(:,6));
589	end
590
591	%OK, now create the new model!
592
593	%take every field from model
594	md2=md1;
595
596	%automatically modify fields
597
598	%loop over model fields
599	model_fields=fields(md1);
600	for i=1:length(model_fields),
601	%get field
602	field=md1.(model_fields{i});
603	fieldsize=size(field);
604	if isobject(field), %recursive call
605	object_fields=fields(md1.(model_fields{i}));
606	for j=1:length(object_fields),
607	%get field
608	field=md1.(model_fields{i}).(object_fields{j});
609	fieldsize=size(field);
610	%size = number of nodes * n
611	if fieldsize(1)==numberofvertices1
612	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
613	elseif (fieldsize(1)==numberofvertices1+1)
614	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
615	%size = number of elements * n
616	elseif fieldsize(1)==numberofelements1
617	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
618	elseif (fieldsize(1)==numberofelements1+1)
619	md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
620	end
621	end
622	else
623	%size = number of nodes * n
624	if fieldsize(1)==numberofvertices1
625	md2.(model_fields{i})=field(pos_node,:);
626	elseif (fieldsize(1)==numberofvertices1+1)
627	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
628	%size = number of elements * n
629	elseif fieldsize(1)==numberofelements1
630	md2.(model_fields{i})=field(pos_elem,:);
631	elseif (fieldsize(1)==numberofelements1+1)
632	md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
633	end
634	end
635	end
636
637	%modify some specific fields
638
639	%Mesh
640	md2.mesh.numberofelements=numberofelements2;
641	md2.mesh.numberofvertices=numberofvertices2;
642	md2.mesh.elements=elements_2;
643
644	%mesh.uppervertex mesh.lowervertex
645	if isa(md1.mesh,'mesh3dprisms'),
646	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
647	pos=find(~isnan(md2.mesh.uppervertex));
648	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
649
650	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
651	pos=find(~isnan(md2.mesh.lowervertex));
652	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
653
654	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
655	pos=find(~isnan(md2.mesh.upperelements));
656	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
657
658	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
659	pos=find(~isnan(md2.mesh.lowerelements));
660	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
661	end
662
663	%Initial 2d mesh
664	if isa(md1.mesh,'mesh3dprisms'),
665	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
666	pos_elem_2d=find(flag_elem_2d);
667	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
668	pos_node_2d=find(flag_node_2d);
669
670	md2.mesh.numberofelements2d=length(pos_elem_2d);
671	md2.mesh.numberofvertices2d=length(pos_node_2d);
672	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
673	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
674	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
675	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
676
677	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
678	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
679	end
680
681	%Edges
682	if(dimension(md.mesh)==2),
683	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
684	%renumber first two columns
685	pos=find(md2.mesh.edges(:,4)~=-1);
686	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
687	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
688	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
689	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
690	%remove edges when the 2 vertices are not in the domain.
691	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
692	%Replace all zeros by -1 in the last two columns
693	pos=find(md2.mesh.edges(:,3)==0);
694	md2.mesh.edges(pos,3)=-1;
695	pos=find(md2.mesh.edges(:,4)==0);
696	md2.mesh.edges(pos,4)=-1;
697	%Invert -1 on the third column with last column (Also invert first two columns!!)
698	pos=find(md2.mesh.edges(:,3)==-1);
699	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
700	md2.mesh.edges(pos,4)=-1;
701	values=md2.mesh.edges(pos,2);
702	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
703	md2.mesh.edges(pos,1)=values;
704	%Finally remove edges that do not belong to any element
705	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
706	md2.mesh.edges(pos,:)=[];
707	end
708	end
709
710	%Penalties
711	if ~isnan(md2.stressbalance.vertex_pairing),
712	for i=1:size(md1.stressbalance.vertex_pairing,1);
713	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
714	end
715	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
716	end
717	if ~isnan(md2.masstransport.vertex_pairing),
718	for i=1:size(md1.masstransport.vertex_pairing,1);
719	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
720	end
721	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
722	end
723
724	%recreate segments
725	if isa(md1.mesh,'mesh2d') \| isa(md1.mesh','mesh3dsurface'),
726	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
727	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
728	md2.mesh.segments=contourenvelope(md2.mesh);
729	md2.mesh.vertexonboundary=zeros(numberofvertices2,1);
730	md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
731	else
732	%First do the connectivity for the contourenvelope in 2d
733	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
734	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
735	segments=contourenvelope(md2.mesh);
736	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1);
737	md2.mesh.vertexonboundary(segments(:,1:2))=1;
738	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
739	%Then do it for 3d as usual
740	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
741	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
742	end
743
744	%Boundary conditions: Dirichlets on new boundary
745	%Catch the elements that have not been extracted
746	orphans_elem=find(~flag_elem);
747	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
748	%Figure out which node are on the boundary between md2 and md1
749	nodestoflag1=intersect(orphans_node,pos_node);
750	nodestoflag2=Pnode(nodestoflag1);
751	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>1 & numel(md1.stressbalance.spcvz)>1,
752	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
753	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
754	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
755	else
756	md2.stressbalance.spcvx(nodestoflag2)=NaN;
757	md2.stressbalance.spcvy(nodestoflag2)=NaN;
758	disp(' ')
759	disp('!! extract warning: spc values should be checked !!')
760	disp(' ')
761	end
762	%put 0 for vz
763	md2.stressbalance.spcvz(nodestoflag2)=0;
764	end
765	if ~isnan(md1.thermal.spctemperature),
766	md2.thermal.spctemperature(nodestoflag2,1)=1;
767	end
768
769	%Results fields
770	if isstruct(md1.results),
771	md2.results=struct();
772	solutionfields=fields(md1.results);
773	for i=1:length(solutionfields),
774	if isstruct(md1.results.(solutionfields{i}))
775	%get subfields
776	% loop over time steps
777	for p=1:length(md1.results.(solutionfields{i}))
778	current = md1.results.(solutionfields{i})(p);
779	solutionsubfields=fields(current);
780	for j=1:length(solutionsubfields),
781	field=md1.results.(solutionfields{i})(p).(solutionsubfields{j});
782	if length(field)==numberofvertices1,
783	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_node);
784	elseif length(field)==numberofelements1,
785	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_elem);
786	else
787	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field;
788	end
789	end
790	end
791	else
792	field=md1.results.(solutionfields{i});
793	if length(field)==numberofvertices1,
794	md2.results.(solutionfields{i})=field(pos_node);
795	elseif length(field)==numberofelements1,
796	md2.results.(solutionfields{i})=field(pos_elem);
797	else
798	md2.results.(solutionfields{i})=field;
799	end
800	end
801	end
802	end
803
804	%OutputDefinitions fields
805	for i=1:length(md1.outputdefinition.definitions),
806	if isobject(md1.outputdefinition.definitions{i})
807	%get subfields
808	solutionsubfields=fields(md1.outputdefinition.definitions{i});
809	for j=1:length(solutionsubfields),
810	field=md1.outputdefinition.definitions{i}.(solutionsubfields{j});
811	if length(field)==numberofvertices1,
812	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node);
813	elseif length(field)==numberofelements1,
814	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem);
815	end
816	end
817	end
818	end
819
820	%Keep track of pos_node and pos_elem
821	md2.mesh.extractedvertices=pos_node;
822	md2.mesh.extractedelements=pos_elem;
823	end % }}}
824	function md2 = refine(md) % {{{
825	%refine - split all triangles into 3 to refine the mesh everywhere
826	%
827	% This function only works for 2d triangle meshes
828	%
829	% Usage:
830	% md2=refine(md);
831	%
832	% See also: EXTRUDE, COLLAPSE, EXTRACT
833
834	%Check incoming
835	if ~strcmp(elementtype(md.mesh),'Tria')
836	error('not supported for 3d meshes');
837	end
838
839	%copy model
840	md2=md;
841
842	disp('Getting edges');
843	%initialization of some variables
844	nbe = md.mesh.numberofelements;
845	nbv = md.mesh.numberofvertices;
846	index = md.mesh.elements;
847	elementslist=1:nbe;
848	%1: list of edges
849	edges=[index(:,[1,2]); index(:,[2,3]); index(:,[3,1])];
850	%2: find unique edges
851	[edges,I,J]=unique(sort(edges,2),'rows');
852	%3: unique edge numbers
853	vec=J;
854	%4: unique edges numbers in each triangle (2 triangles sharing the same edge will have the same edge number)
855	edges_tria=[vec(elementslist+nbe) vec(elementslist+2*nbe) vec(elementslist)];
856
857	% We divide each element as follows
858	%
859	% e2
860	% n1 ------------+------------ n3
861	% \ / \ /
862	% \ 1 / \ 3 /
863	% \ / \ /
864	% \ / 2 \ /
865	% \ / \ /
866	% e3 +____________\/ e1
867	% \ /
868	% \ /
869	% \ 4 /
870	% \ /
871	% \ /
872	% n2
873
874	%Create new coordinates
875	disp('Remeshing...');
876	x_edges = 0.5*(md.mesh.x(edges(:,1)) + md.mesh.x(edges(:,2)));
877	y_edges = 0.5*(md.mesh.y(edges(:,1)) + md.mesh.y(edges(:,2)));
878	md2.mesh.x = [md2.mesh.x;x_edges];
879	md2.mesh.y = [md2.mesh.y;y_edges];
880	md2.mesh.elements = [...
881	index(:,1) nbv+edges_tria(:,3) nbv+edges_tria(:,2);...
882	nbv+edges_tria(:,2) nbv+edges_tria(:,3) nbv+edges_tria(:,1);...
883	nbv+edges_tria(:,2) nbv+edges_tria(:,1) index(:,3);...
884	nbv+edges_tria(:,3) index(:,2) nbv+edges_tria(:,1)];
885	md2.mesh.numberofelements = 4*nbe;
886	md2.mesh.numberofvertices = nbv + size(edges,1);
887	disp([' Old number of elements: ' num2str(nbe)]);
888	disp([' New number of elements: ' num2str(4*nbe)]);
889
890	disp('Interpolate all fields');
891	numberofvertices1 = md.mesh.numberofvertices;
892	numberofelements1 = md.mesh.numberofelements;
893	nbv2 = md2.mesh.numberofvertices;
894	%Create transformation vectors
895	nbedges = size(edges,1);
896	Pelem = sparse(1:4nbe,repmat([1:nbe],1,4),ones(4nbe,1),4*nbe,nbe);
897	Pnode = sparse([1:nbv,repmat([nbv+1:nbv+nbedges],1,2)],[1:nbv edges(:)'],[ones(nbv,1);1/2ones(2nbedges,1)],md2.mesh.numberofvertices,nbv);
898	%loop over model fields
899	model_fields=setxor(fields(md),{'mesh'});
900	%remove mesh from this field
901	for i=1:length(model_fields),
902	%get field
903	field=md.(model_fields{i});
904	fieldsize=size(field);
905	if isobject(field), %recursive call
906	object_fields=fields(md.(model_fields{i}));
907	for j=1:length(object_fields),
908	%get field
909	field=md.(model_fields{i}).(object_fields{j});
910	fieldsize=size(field);
911	%size = number of nodes * n
912	if fieldsize(1)==numberofvertices1
913	md2.(model_fields{i}).(object_fields{j})=Pnode*field;
914	elseif (fieldsize(1)==numberofvertices1+1)
915	md2.(model_fields{i}).(object_fields{j})=[Pnode*field(1:end-1,:); field(end,:)];
916	%size = number of elements * n
917	elseif fieldsize(1)==numberofelements1
918	md2.(model_fields{i}).(object_fields{j})=Pelem*field;
919	elseif (fieldsize(1)==numberofelements1+1)
920	md2.(model_fields{i}).(object_fields{j})=[Pelem*field(1:end-1,:); field(end,:)];
921	end
922	end
923	else
924	%size = number of nodes * n
925	if fieldsize(1)==numberofvertices1
926	md2.(model_fields{i})=Pnode*field;
927	elseif (fieldsize(1)==numberofvertices1+1)
928	md2.(model_fields{i})=[Pnode*field(1:end-1,:); field(end,:)];
929	%size = number of elements * n
930	elseif fieldsize(1)==numberofelements1
931	md2.(model_fields{i})=Pelem*field;
932	elseif (fieldsize(1)==numberofelements1+1)
933	md2.(model_fields{i})=[Pelem*field(1:end-1,:); field(end,:)];
934	end
935	end
936	end
937
938	end % }}}
939	function md = extrude(md,varargin) % {{{
940	%EXTRUDE - vertically extrude a 2d mesh
941	%
942	% vertically extrude a 2d mesh and create corresponding 3d mesh.
943	% The vertical distribution can:
944	% - follow a polynomial law
945	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
946	% - be discribed by a list of coefficients (between 0 and 1)
947	%
948	%
949	% Usage:
950	% md=extrude(md,numlayers,extrusionexponent);
951	% md=extrude(md,numlayers,lowerexponent,upperexponent);
952	% md=extrude(md,listofcoefficients);
953	%
954	% Example:
955	% md=extrude(md,15,1.3);
956	% md=extrude(md,15,1.3,1.2);
957	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
958	%
959	% See also: MODELEXTRACT, COLLAPSE
960
961	%some checks on list of arguments
962	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
963	help extrude;
964	error('extrude error message');
965	end
966	if numel(md.geometry.base)~=md.mesh.numberofvertices \|\| numel(md.geometry.surface)~=md.mesh.numberofvertices
967	error('model has not been parameterized yet: base and/or surface not set');
968	end
969
970	%Extrude the mesh
971	if nargin==2, %list of coefficients
972	clist=varargin{1};
973	if any(clist<0) \| any(clist>1),
974	error('extrusioncoefficients must be between 0 and 1');
975	end
976	extrusionlist=sort(unique([clist(:);0;1]));
977	numlayers=length(extrusionlist);
978	elseif nargin==3, %one polynomial law
979	if varargin{2}<=0,
980	help extrude;
981	error('extrusionexponent must be >=0');
982	end
983	numlayers=varargin{1};
984	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
985	elseif nargin==4, %two polynomial laws
986	numlayers=varargin{1};
987	lowerexp=varargin{2};
988	upperexp=varargin{3};
989
990	if varargin{2}<=0 \| varargin{3}<=0,
991	help extrude;
992	error('lower and upper extrusionexponents must be >=0');
993	end
994
995	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
996	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
997	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
998
999	end
1000
1001	if numlayers<2,
1002	error('number of layers should be at least 2');
1003	end
1004	if strcmp(md.mesh.domaintype(),'3D')
1005	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
1006	end
1007
1008	%Initialize with the 2d mesh
1009	mesh2d = md.mesh;
1010	md.mesh=mesh3dprisms();
1011	md.mesh.x = mesh2d.x;
1012	md.mesh.y = mesh2d.y;
1013	md.mesh.elements = mesh2d.elements;
1014	md.mesh.numberofelements = mesh2d.numberofelements;
1015	md.mesh.numberofvertices = mesh2d.numberofvertices;
1016
1017	md.mesh.lat = mesh2d.lat;
1018	md.mesh.long = mesh2d.long;
1019	md.mesh.epsg = mesh2d.epsg;
1020	md.mesh.scale_factor = mesh2d.scale_factor;
1021
1022	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
1023	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
1024	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
1025	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
1026
1027	md.mesh.extractedvertices = mesh2d.extractedvertices;
1028	md.mesh.extractedelements = mesh2d.extractedelements;
1029
1030	x3d=[];
1031	y3d=[];
1032	z3d=[]; %the lower node is on the bed
1033	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
1034	bed3d=md.geometry.base;
1035
1036	%Create the new layers
1037	for i=1:numlayers,
1038	x3d=[x3d; md.mesh.x];
1039	y3d=[y3d; md.mesh.y];
1040	%nodes are distributed between bed and surface accordingly to the given exponent
1041	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
1042	end
1043	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
1044
1045	%Extrude elements
1046	elements3d=[];
1047	for i=1:numlayers-1,
1048	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
1049	end
1050	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
1051
1052	%Keep a trace of lower and upper nodes
1053	lowervertex=NaN*ones(number_nodes3d,1);
1054	uppervertex=NaN*ones(number_nodes3d,1);
1055	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
1056	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
1057	md.mesh.lowervertex=lowervertex;
1058	md.mesh.uppervertex=uppervertex;
1059
1060	%same for lower and upper elements
1061	lowerelements=NaN*ones(number_el3d,1);
1062	upperelements=NaN*ones(number_el3d,1);
1063	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
1064	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
1065	md.mesh.lowerelements=lowerelements;
1066	md.mesh.upperelements=upperelements;
1067
1068	%Save old mesh
1069	md.mesh.x2d=md.mesh.x;
1070	md.mesh.y2d=md.mesh.y;
1071	md.mesh.elements2d=md.mesh.elements;
1072	md.mesh.numberofelements2d=md.mesh.numberofelements;
1073	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
1074
1075	%Build global 3d mesh
1076	md.mesh.elements=elements3d;
1077	md.mesh.x=x3d;
1078	md.mesh.y=y3d;
1079	md.mesh.z=z3d;
1080	md.mesh.numberofelements=number_el3d;
1081	md.mesh.numberofvertices=number_nodes3d;
1082	md.mesh.numberoflayers=numlayers;
1083
1084	%Ok, now deal with the other fields from the 2d mesh:
1085
1086	%bedinfo and surface info
1087	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
1088	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
1089	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
1090
1091	%lat long
1092	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
1093	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
1094	md.mesh.scale_factor=project3d(md,'vector',md.mesh.scale_factor,'type','node');
1095
1096	md.geometry=extrude(md.geometry,md);
1097	md.friction = extrude(md.friction,md);
1098	md.inversion = extrude(md.inversion,md);
1099	md.smb = extrude(md.smb,md);
1100	md.initialization = extrude(md.initialization,md);
1101
1102	md.flowequation=md.flowequation.extrude(md);
1103	md.stressbalance=extrude(md.stressbalance,md);
1104	md.thermal=md.thermal.extrude(md);
1105	md.masstransport=md.masstransport.extrude(md);
1106	md.levelset=extrude(md.levelset,md);
1107	md.calving=extrude(md.calving,md);
1108	md.frontalforcings=extrude(md.frontalforcings,md);
1109	md.hydrology = extrude(md.hydrology,md);
1110	md.solidearth = extrude(md.solidearth,md);
1111	md.dsl = extrude(md.dsl,md);
1112
1113	%connectivity
1114	if ~isnan(md.mesh.elementconnectivity)
1115	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
1116	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
1117	for i=2:numlayers-1,
1118	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
1119	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
1120	end
1121	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
1122	end
1123
1124	md.materials=extrude(md.materials,md);
1125	md.damage=extrude(md.damage,md);
1126	md.mask=extrude(md.mask,md);
1127	md.qmu=extrude(md.qmu,md);
1128	md.basalforcings=extrude(md.basalforcings,md);
1129	md.outputdefinition=extrude(md.outputdefinition,md);
1130
1131	%increase connectivity if less than 25:
1132	if md.mesh.average_vertex_connectivity<=25,
1133	md.mesh.average_vertex_connectivity=100;
1134	end
1135	end % }}}
1136	function md = structtomodel(md,structmd) % {{{
1137
1138	if ~isstruct(structmd) error('input model is not a structure'); end
1139
1140	%loaded model is a struct, initialize output and recover all fields
1141	md = structtoobj(model,structmd);
1142
1143	%Old field now classes
1144	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
1145	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
1146
1147	%Field name change
1148	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
1149	if isfield(structmd,'p'), md.friction.p=structmd.p; end
1150	if isfield(structmd,'q'), md.friction.q=structmd.p; end
1151	if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
1152	if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
1153	if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
1154	if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
1155	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
1156	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
1157	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
1158	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
1159	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
1160	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
1161	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
1162	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
1163	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
1164	if isfield(structmd,'g'), md.constants.g=structmd.g; end
1165	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
1166	if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
1167	if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
1168	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
1169	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
1170	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
1171	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
1172	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
1173	if isfield(structmd,'riftproperties'), %old implementation
1174	md.rifts=rifts();
1175	md.rifts.riftproperties=structmd.riftproperties;
1176	md.rifts.riftstruct=structmd.rifts;
1177	md.rifts.riftproperties=structmd.riftinfo;
1178	end
1179	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
1180	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
1181	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
1182	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
1183	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
1184	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
1185	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
1186	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
1187	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
1188	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
1189	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
1190	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
1191	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
1192	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
1193	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
1194	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
1195	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
1196	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
1197	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
1198	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
1199	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
1200	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
1201	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
1202	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
1203	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
1204	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
1205	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
1206	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
1207	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
1208	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
1209	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
1210	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
1211	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
1212	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
1213	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
1214	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
1215	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
1216	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
1217	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
1218	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
1219	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
1220	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
1221	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
1222	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
1223	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
1224	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
1225	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
1226	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
1227	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
1228	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
1229	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
1230	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
1231	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
1232	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
1233	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
1234	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
1235	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
1236	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
1237	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
1238	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
1239	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
1240	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
1241	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
1242	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
1243	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
1244	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
1245	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
1246	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
1247	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
1248	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
1249	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
1250	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
1251	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
1252	if isfield(structmd,'scale_factor'), md.mesh.scale_factor=structmd.scale_factor; end
1253	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
1254	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
1255	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
1256	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
1257	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
1258	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
1259	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
1260	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
1261	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
1262	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
1263	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
1264	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
1265	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
1266	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
1267	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
1268	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
1269	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
1270	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
1271	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
1272	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
1273	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
1274	if isfield(structmd,'edges'),
1275	md.mesh.edges=structmd.edges;
1276	md.mesh.edges(isnan(md.mesh.edges))=-1;
1277	end
1278	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
1279	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
1280	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
1281	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
1282	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
1283	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
1284
1285	if isnumeric(md.verbose),
1286	md.verbose=verbose;
1287	end
1288
1289	if isfield(structmd,'spcvelocity'),
1290	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
1291	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
1292	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1293	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
1294	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
1295	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
1296	end
1297	if isfield(structmd,'spcvx'),
1298	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
1299	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
1300	end
1301	if isfield(structmd,'spcvy'),
1302	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
1303	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
1304	end
1305	if isfield(structmd,'spcvz'),
1306	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1307	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
1308	end
1309	if isfield(structmd,'pressureload'),
1310	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
1311	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
1312	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
1313	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
1314	end
1315	end
1316	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
1317	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
1318	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
1319	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
1320	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
1321	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
1322	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
1323	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
1324	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
1325	end
1326	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
1327	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
1328	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
1329	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
1330	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
1331	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
1332	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
1333	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
1334	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
1335	end
1336	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
1337	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
1338	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1339	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1340	end
1341	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1342	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1343	if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
1344	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1345	end
1346	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1347	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1348	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1349	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1350	end
1351	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1352	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1353	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1354	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1355	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1356	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1357	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1358	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1359	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1360	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1361	end
1362
1363	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1364	md.thermal.stabilization=2;
1365	md.masstransport.stabilization=1;
1366	md.balancethickness.stabilization=1;
1367	end
1368	if isnumeric(md.masstransport.hydrostatic_adjustment)
1369	if md.masstransport.hydrostatic_adjustment==269,
1370	md.masstransport.hydrostatic_adjustment='Incremental';
1371	else
1372	md.masstransport.hydrostatic_adjustment='Absolute';
1373	end
1374	end
1375
1376	%New fields
1377	if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
1378	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1379	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1380	end
1381	if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
1382	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1383	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1384	end
1385	if ~isfield(structmd,'diagnostic_ref');
1386	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1387	end
1388	if ~isfield(structmd,'loadingforce');
1389	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1390	end
1391
1392	%2013 August 9
1393	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1394	disp('Recovering old prognostic class');
1395	md.masstransport=masstransport(structmd.prognostic);
1396	end
1397	%2013 August 9
1398	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
1399	disp('Recovering old diagnostic class');
1400	md.stressbalance=stressbalance(structmd.diagnostic);
1401	end
1402	%2014 January 9th
1403	if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
1404	disp('Recovering old surfaceforcings class');
1405	mass_balance=structmd.surfaceforcings.mass_balance;
1406	md.smb=SMB();
1407	md.smb.mass_balance=mass_balance;
1408	end
1409	%2015 September 10
1410	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
1411	disp('Recovering old SMB class');
1412	md.smb=SMBforcing(structmd.surfaceforcings);
1413	end
1414	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
1415	disp('Recovering old SMBhenning class');
1416	md.smb=SMBhenning(structmd.surfaceforcings);
1417	end
1418	if isfield(structmd,'slr'),
1419	disp('Recovering old slr class');
1420	if isfield(structmd.slr,'sealevel'),
1421	md.solidearth.sealevel=structmd.slr.sealevel;
1422	end
1423	md.solidearth.planetradius=structmd.slr.planetradius;
1424	md.solidearth.requested_outputs=structmd.slr.requested_outputs;
1425	md.solidearth.transitions=structmd.slr.transitions;
1426
1427	md.solidearth.transitions=structmd.slr.transitions;
1428	md.solidearth.settings.reltol=structmd.slr.reltol;
1429	md.solidearth.settings.abstol=structmd.slr.abstol;
1430	md.solidearth.settings.maxiter=structmd.slr.maxiter;
1431	md.solidearth.settings.rigid=structmd.slr.rigid;
1432	md.solidearth.settings.elastic=structmd.slr.elastic;
1433	md.solidearth.settings.rotation=structmd.slr.rotation;
1434	md.solidearth.settings.runfrequency=structmd.slr.geodetic_run_frequency;
1435	md.solidearth.settings.computesealevelchange=structmd.slr.geodetic;
1436	md.solidearth.settings.degacc=structmd.slr.degacc;
1437	md.solidearth.settings.horiz=structmd.slr.horiz;
1438	md.solidearth.settings.ocean_area_scaling=structmd.slr.ocean_area_scaling;
1439
1440	md.solidearth.surfaceload.icethicknesschange=structmd.slr.deltathickness;
1441	md.solidearth.surfaceload.waterheightchange=structmd.slr.hydro_rate;
1442
1443	md.solidearth.lovenumbers.h=structmd.slr.love_h;
1444	md.solidearth.lovenumbers.k=structmd.slr.love_k;
1445	md.solidearth.lovenumbers.l=structmd.slr.love_l;
1446	md.solidearth.lovenumbers.th=structmd.slr.tide_love_h;
1447	md.solidearth.lovenumbers.tk=structmd.slr.tide_love_k;
1448	md.solidearth.lovenumbers.tk2secular=structmd.slr.fluid_love;
1449
1450	md.solidearth.rotational.equatorialmoi=structmd.slr.equatorial_moi;
1451	md.solidearth.rotational.polarmoi=structmd.slr.polar_moi;
1452	md.solidearth.rotational.angularvelocity=structmd.slr.angular_velocity;
1453	end
1454	end% }}}
1455	function md = tetras(md,varargin) % {{{
1456	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1457	%
1458	% Usage:
1459	% md=tetra(md)
1460
1461	if ~isa(md.mesh,'mesh3dprisms')
1462	error('mesh is not a 3d prismatic mesh');
1463	end
1464
1465	%Initialize tetra mesh
1466	md.mesh=mesh3dtetras(md.mesh);
1467
1468	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
1469	steiner = 0;
1470	nbv = md.mesh.numberofvertices;
1471	nbt = 3*md.mesh.numberofelements;
1472	elements = zeros(nbt,4);
1473	for i=1:md.mesh.numberofelements
1474	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
1475	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
1476	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1477	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1478	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1479	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1480	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1481	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1482	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
1483	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
1484	elements(end+1,:) = [v2 v3 v5 v7];
1485	elements(end+1,:) = [v3 v5 v6 v7];
1486	elements(end+1,:) = [v1 v3 v6 v7];
1487	elements(end+1,:) = [v1 v4 v6 v7];
1488	elements(end+1,:) = [v4 v5 v6 v7];
1489	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1490	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
1491	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1492	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1493	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1494	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1495	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
1496	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1497	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1498	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1499	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1500	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
1501	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1502	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1503	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1504	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
1505	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1506	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1507	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
1508	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1509	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1510	elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
1511	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1512	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1513	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1514	elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
1515	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1516	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
1517	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1518	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1519	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1520	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1521	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1522	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1523	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
1524	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
1525	elements(end+1,:) = [v2 v5 v6 v7];
1526	elements(end+1,:) = [v2 v3 v6 v7];
1527	elements(end+1,:) = [v3 v4 v6 v7];
1528	elements(end+1,:) = [v1 v3 v4 v7];
1529	elements(end+1,:) = [v4 v5 v6 v7];
1530	else
1531	error('Case not supported'); %not supposed to happen!
1532	end
1533	%Reorder elements to make sure they are direct
1534	for j=1:3
1535	element = elements(3*(i-1)+j,:);
1536	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
1537	if det(matrix)>0,
1538	elements(3*(i-1)+j,1)=element(2);
1539	elements(3*(i-1)+j,2)=element(1);
1540	end
1541	end
1542	end
1543	%%Split in 3 tetras
1544	%subelement1 = [1 2 3 5];
1545	%subelement2 = [4 6 5 1];
1546	%subelement3 = [5 6 3 1];
1547	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
1548	if steiner==0,
1549	disp('No Steiner point required to split prismatic mesh into tets');
1550	else
1551	disp([num2str(steiner) ' Steiner points had to be included'])
1552	error('Steiner point not supported yet');
1553	end
1554
1555	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1556
1557	md.mesh.elements=elements;
1558	md.mesh.numberofelements=size(elements,1);
1559
1560	%p and q (same deal, except for element that are on the bedrock: )
1561	if ~isnan(md.friction.p),
1562	md.friction.p=md.friction.p(pos_elements);
1563	md.friction.q=md.friction.q(pos_elements);
1564	end
1565
1566	%elementstype
1567	if ~isnan(md.flowequation.element_equation)
1568	oldelements_type=md.flowequation.element_equation;
1569	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1570	end
1571
1572	%connectivity
1573	md.mesh.elementconnectivity=NaN;
1574
1575	%materials
1576	if ~isnan(md.materials.rheology_n),
1577	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1578	end
1579
1580	%increase connectivity if less than 25:
1581	if md.mesh.average_vertex_connectivity<=25,
1582	md.mesh.average_vertex_connectivity=100;
1583	end
1584	end % }}}
1585	function disp(self) % {{{
1586	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
1587	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
1588	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1589	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
1590	disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
1591	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
1592	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
1593	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
1594	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
1595	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
1596	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
1597	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
1598	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
1599	disp(sprintf('%19s: %-22s -- %s','solidearth' ,['[1x1 ' class(self.solidearth) ']'],'solidearth inputs and settings'));
1600	disp(sprintf('%19s: %-22s -- %s','dsl' ,['[1x1 ' class(self.dsl) ']'],'dynamic sea-level '));
1601	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
1602	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
1603	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
1604	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
1605	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of CPUs...)'));
1606	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
1607	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
1608	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
1609	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
1610	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
1611	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
1612	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
1613	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parHwoameters for transient solution'));
1614	disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
1615	disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
1616	disp(sprintf('%19s: %-22s -- %s','frontalforcings' ,['[1x1 ' class(self.frontalforcings) ']'],'parameters for frontalforcings'));
1617	disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
1618	disp(sprintf('%19s: %-22s -- %s','love' ,['[1x1 ' class(self.love) ']'],'parameters for love solution'));
1619	disp(sprintf('%19s: %-22s -- %s','sampling' ,['[1x1 ' class(self.sampling) ']'],'parameters for stochastic sampler'));
1620	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
1621	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
1622	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'Dakota properties'));
1623	disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
1624	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
1625	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
1626	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
1627	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
1628	end % }}}
1629	function memory(self) % {{{
1630
1631	disp(sprintf('\nMemory imprint:\n'));
1632
1633	fields=properties('model');
1634	mem=0;
1635
1636	for i=1:length(fields),
1637	field=self.(fields{i});
1638	s=whos('field');
1639	mem=mem+s.bytes/1e6;
1640	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1641	end
1642	disp(sprintf('%19s--%10s','--------------','--------------'));
1643	disp(sprintf('%19s: %g Mb','Total',mem));
1644	end % }}}
1645	function netcdf(self,filename) % {{{
1646	%NETCDF - save model as netcdf
1647	%
1648	% Usage:
1649	% netcdf(md,filename)
1650	%
1651	% Example:
1652	% netcdf(md,'model.nc');
1653
1654	disp('Saving model as NetCDF');
1655	%1. Create NetCDF file
1656	ncid=netcdf.create(filename,'CLOBBER');
1657	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1658	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
1659	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1660	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1661
1662	%Preallocate variable id, needed to write variables in netcdf file
1663	var_id=zeros(1000,1);%preallocate
1664
1665	for step=1:2,
1666	counter=0;
1667	[var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
1668	if step==1, netcdf.endDef(ncid); end
1669	end
1670
1671	if counter>1000,
1672	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1673	end
1674
1675	netcdf.close(ncid)
1676	end % }}}
1677	function xylim(self) % {{{
1678
1679	xlim([min(self.mesh.x) max(self.mesh.x)]);
1680	ylim([min(self.mesh.y) max(self.mesh.y)])
1681	end % }}}
1682	function md=upload(md) % {{{
1683	%the goal of this routine is to upload the model onto a server, and to empty it.
1684	%So first, save the model with a unique name and upload the file to the server:
1685	random_part=fix(rand(1)*10000);
1686	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1687	eval(['save ' id ' md']);
1688
1689	%Now, upload the file:
1690	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1691
1692	%Now, empty this model of everything except settings, and record name of file we just uploaded!
1693	settings_back=md.settings;
1694	md=model();
1695	md.settings=settings_back;
1696	md.settings.upload_filename=id;
1697
1698	%get locally rid of file that was uploaded
1699	eval(['delete ' id]);
1700
1701	end % }}}
1702	function md=download(md) % {{{
1703
1704	%the goal of this routine is to download the internals of the current model from a server, because
1705	%this model is empty, except for the settings which tell us where to go and find this model!
1706
1707	%Download the file:
1708	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1709
1710	name=md.settings.upload_filename;
1711
1712	%Now, load this model:
1713	md=loadmodel(md.settings.upload_filename);
1714
1715	%get locally rid of file that was downloaded
1716	eval(['delete ' name]);
1717
1718	end % }}}
1719	function savemodeljs(md,modelname,websiteroot,varargin) % {{{
1720
1721	%the goal of this routine is to save the model as a javascript array that can be included in any html
1722	%file:
1723
1724	options=pairoptions(varargin{:});
1725	optimization=getfieldvalue(options,'optimize',0);
1726
1727
1728	%disp:
1729	disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
1730
1731	%open file for writing and declare the model:
1732	fid=fopen([websiteroot '/js/' modelname '.js'],'w');
1733	fprintf(fid,'var %s=new model();\n',modelname);
1734
1735	%now go through all the classes and fwrite all the corresponding fields:
1736
1737	fields=properties('model');
1738	for i=1:length(fields),
1739	field=fields{i};
1740
1741	%Some properties do not need to be saved
1742	if ismember(field,{'results','cluster' }),
1743	continue;
1744	end
1745
1746	%some optimization:
1747	if optimization==1,
1748	%optimize for plotting only:
1749	if ~ismember(field,{'geometry','mesh','mask'}),
1750	continue;
1751	end
1752	end
1753
1754	%Check that current field is an object
1755	if ~isobject(md.(field))
1756	error(['field ''' char(field) ''' is not an object']);
1757	end
1758
1759	%savemodeljs for current object
1760	%disp(['javascript saving ' field '...']);
1761	savemodeljs(md.(field),fid,modelname);
1762	end
1763
1764	%done, close file:
1765	fclose(fid);
1766	end
1767	end
1768	end

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