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

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

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

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