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source: issm/trunk-jpl/src/m/classes/model.m@ 17563

Last change on this file since 17563 was 17563, checked in by Mathieu Morlighem, 11 years ago
BUG: fixing some tests now that subclasses are used for md.mesh
File size: 62.3 KB

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

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