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source: issm/trunk-jpl/src/m/classes/model.m@ 19124

Last change on this file since 19124 was 19124, checked in by Mathieu Morlighem, 10 years ago
CHG: upperelements and lowerelements are only for 3d prisms
File size: 61.9 KB

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

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