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source: issm/trunk-jpl/src/m/classes/model.m@ 17435

Last change on this file since 17435 was 17435, checked in by jbondzio, 11 years ago
ADD: extrusion of masstransport.calvingrate
File size: 59.9 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	end% }}}
114	end
115	methods
116	function md = model(varargin) % {{{
117
118	switch nargin
119	case 0
120	md=setdefaultparameters(md);
121	otherwise
122	error('model constructor error message: 0 of 1 argument only in input.');
123	end
124	end
125	%}}}
126	function md = checkmessage(md,string) % {{{
127	if(nargout~=1) error('wrong usage, model must be an output'); end
128	disp(['model not consistent: ' string]);
129	md.private.isconsistent=false;
130	end
131	%}}}
132	function md = collapse(md)% {{{
133	%COLLAPSE - collapses a 3d mesh into a 2d mesh
134	%
135	% This routine collapses a 3d model into a 2d model
136	% and collapses all the fileds of the 3d model by
137	% taking their depth-averaged values
138	%
139	% Usage:
140	% md=collapse(md)
141	%
142	% See also: EXTRUDE, MODELEXTRACT
143
144	%Check that the model is really a 3d model
145	if ~md.mesh.dimension==3,
146	error('collapse error message: only 3d mesh can be collapsed')
147	end
148
149	%Start with changing alle the fields from the 3d mesh
150
151	%drag is limited to nodes that are on the bedrock.
152	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
153
154	%p and q (same deal, except for element that are on the bedrock: )
155	md.friction.p=project2d(md,md.friction.p,1);
156	md.friction.q=project2d(md,md.friction.q,1);
157
158	%observations
159	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
160	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
161	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
162	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
163	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
164	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
165	if ~isnan(md.surfaceforcings.mass_balance),
166	md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers);
167	end;
168	if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
169
170	%results
171	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
172	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
173	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
174	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
175	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
176
177	%gia
178	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
179	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
180
181	%bedinfo and surface info
182	md.mesh.elementonbed=ones(md.mesh.numberofelements2d,1);
183	md.mesh.elementonsurface=ones(md.mesh.numberofelements2d,1);
184	md.mesh.vertexonbed=ones(md.mesh.numberofvertices2d,1);
185	md.mesh.vertexonsurface=ones(md.mesh.numberofvertices2d,1);
186
187	%elementstype
188	if ~isnan(md.flowequation.element_equation)
189	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
190	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
191	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
192	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
193	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
194	end
195
196	%boundary conditions
197	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
198	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
199	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
200	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
201	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
202	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
203	md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers)
204	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
205
206	%materials
207	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
208	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
209
210	%damage:
211	md.damage.D=DepthAverage(md,md.damage.D);
212
213	%special for thermal modeling:
214	md.basalforcings.melting_rate=project2d(md,md.basalforcings.melting_rate,1);
215	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
216
217	%update of connectivity matrix
218	md.mesh.average_vertex_connectivity=25;
219
220	%Collapse the mesh
221	nodes2d=md.mesh.numberofvertices2d;
222	elements2d=md.mesh.numberofelements2d;
223
224	%parameters
225	md.geometry.surface=project2d(md,md.geometry.surface,1);
226	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
227	md.geometry.bed=project2d(md,md.geometry.bed,1);
228	md.geometry.bathymetry=project2d(md,md.geometry.bathymetry,1);
229	md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
230	md.mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
231	md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
232	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
233
234	%lat long
235	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
236	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
237
238	%Initialize with the 2d mesh
239	md.mesh.x=md.mesh.x2d;
240	md.mesh.y=md.mesh.y2d;
241	md.mesh.z=zeros(size(md.mesh.x2d));
242	md.mesh.numberofvertices=md.mesh.numberofvertices2d;
243	md.mesh.numberofelements=md.mesh.numberofelements2d;
244	md.mesh.elements=md.mesh.elements2d;
245
246	%Keep a trace of lower and upper nodes
247	md.mesh.lowervertex=NaN;
248	md.mesh.uppervertex=NaN;
249	md.mesh.lowerelements=NaN;
250	md.mesh.upperelements=NaN;
251
252	%Remove old mesh
253	md.mesh.x2d=NaN;
254	md.mesh.y2d=NaN;
255	md.mesh.elements2d=NaN;
256	md.mesh.numberofelements2d=md.mesh.numberofelements;
257	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
258	md.mesh.numberoflayers=0;
259
260	%Update mesh type
261	md.mesh.dimension=2;
262	end % }}}
263	function md2 = extract(md,area) % {{{
264	%extract - extract a model according to an Argus contour or flag list
265	%
266	% This routine extracts a submodel from a bigger model with respect to a given contour
267	% md must be followed by the corresponding exp file or flags list
268	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
269	% If user wants every element outside the domain to be
270	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
271	% an empty string '' will be considered as an empty domain
272	% a string 'all' will be considered as the entire domain
273	%
274	% Usage:
275	% md2=extract(md,area);
276	%
277	% Examples:
278	% md2=extract(md,'Domain.exp');
279	%
280	% See also: EXTRUDE, COLLAPSE
281
282	%copy model
283	md1=md;
284
285	%some checks
286	if ((nargin~=2) \| (nargout~=1)),
287	help extract
288	error('extract error message: bad usage');
289	end
290
291	%get elements that are inside area
292	flag_elem=FlagElements(md1,area);
293	if ~any(flag_elem),
294	error('extracted model is empty');
295	end
296
297	%kick out all elements with 3 dirichlets
298	spc_elem=find(~flag_elem);
299	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
300	flag=ones(md1.mesh.numberofvertices,1);
301	flag(spc_node)=0;
302	pos=find(sum(flag(md1.mesh.elements),2)==0);
303	flag_elem(pos)=0;
304
305	%extracted elements and nodes lists
306	pos_elem=find(flag_elem);
307	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
308
309	%keep track of some fields
310	numberofvertices1=md1.mesh.numberofvertices;
311	numberofelements1=md1.mesh.numberofelements;
312	numberofvertices2=length(pos_node);
313	numberofelements2=length(pos_elem);
314	flag_node=zeros(numberofvertices1,1);
315	flag_node(pos_node)=1;
316
317	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
318	Pelem=zeros(numberofelements1,1);
319	Pelem(pos_elem)=[1:numberofelements2]';
320	Pnode=zeros(numberofvertices1,1);
321	Pnode(pos_node)=[1:numberofvertices2]';
322
323	%renumber the elements (some nodes won't exist anymore)
324	elements_1=md1.mesh.elements;
325	elements_2=elements_1(pos_elem,:);
326	elements_2(:,1)=Pnode(elements_2(:,1));
327	elements_2(:,2)=Pnode(elements_2(:,2));
328	elements_2(:,3)=Pnode(elements_2(:,3));
329	if md1.mesh.dimension==3,
330	elements_2(:,4)=Pnode(elements_2(:,4));
331	elements_2(:,5)=Pnode(elements_2(:,5));
332	elements_2(:,6)=Pnode(elements_2(:,6));
333	end
334
335	%OK, now create the new model!
336
337	%take every field from model
338	md2=md1;
339
340	%automatically modify fields
341
342	%loop over model fields
343	model_fields=fields(md1);
344	for i=1:length(model_fields),
345	%get field
346	field=md1.(model_fields{i});
347	fieldsize=size(field);
348	if isobject(field), %recursive call
349	object_fields=fields(md1.(model_fields{i}));
350	for j=1:length(object_fields),
351	%get field
352	field=md1.(model_fields{i}).(object_fields{j});
353	fieldsize=size(field);
354	%size = number of nodes * n
355	if fieldsize(1)==numberofvertices1
356	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
357	elseif (fieldsize(1)==numberofvertices1+1)
358	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
359	%size = number of elements * n
360	elseif fieldsize(1)==numberofelements1
361	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
362	end
363	end
364	else
365	%size = number of nodes * n
366	if fieldsize(1)==numberofvertices1
367	md2.(model_fields{i})=field(pos_node,:);
368	elseif (fieldsize(1)==numberofvertices1+1)
369	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
370	%size = number of elements * n
371	elseif fieldsize(1)==numberofelements1
372	md2.(model_fields{i})=field(pos_elem,:);
373	end
374	end
375	end
376
377	%modify some specific fields
378
379	%Mesh
380	md2.mesh.numberofelements=numberofelements2;
381	md2.mesh.numberofvertices=numberofvertices2;
382	md2.mesh.elements=elements_2;
383
384	%mesh.uppervertex mesh.lowervertex
385	if md1.mesh.dimension==3
386	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
387	pos=find(~isnan(md2.mesh.uppervertex));
388	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
389
390	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
391	pos=find(~isnan(md2.mesh.lowervertex));
392	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
393
394	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
395	pos=find(~isnan(md2.mesh.upperelements));
396	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
397
398	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
399	pos=find(~isnan(md2.mesh.lowerelements));
400	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
401	end
402
403	%Initial 2d mesh
404	if md1.mesh.dimension==3
405	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
406	pos_elem_2d=find(flag_elem_2d);
407	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
408	pos_node_2d=find(flag_node_2d);
409
410	md2.mesh.numberofelements2d=length(pos_elem_2d);
411	md2.mesh.numberofvertices2d=length(pos_node_2d);
412	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
413	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
414	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
415	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
416
417	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
418	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
419	end
420
421	%Edges
422	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
423	%renumber first two columns
424	pos=find(md2.mesh.edges(:,4)~=-1);
425	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
426	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
427	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
428	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
429	%remove edges when the 2 vertices are not in the domain.
430	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
431	%Replace all zeros by -1 in the last two columns
432	pos=find(md2.mesh.edges(:,3)==0);
433	md2.mesh.edges(pos,3)=-1;
434	pos=find(md2.mesh.edges(:,4)==0);
435	md2.mesh.edges(pos,4)=-1;
436	%Invert -1 on the third column with last column (Also invert first two columns!!)
437	pos=find(md2.mesh.edges(:,3)==-1);
438	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
439	md2.mesh.edges(pos,4)=-1;
440	values=md2.mesh.edges(pos,2);
441	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
442	md2.mesh.edges(pos,1)=values;
443	%Finally remove edges that do not belong to any element
444	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
445	md2.mesh.edges(pos,:)=[];
446	end
447
448	%Penalties
449	if ~isnan(md2.stressbalance.vertex_pairing),
450	for i=1:size(md1.stressbalance.vertex_pairing,1);
451	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
452	end
453	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
454	end
455	if ~isnan(md2.masstransport.vertex_pairing),
456	for i=1:size(md1.masstransport.vertex_pairing,1);
457	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
458	end
459	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
460	end
461
462	%recreate segments
463	if md1.mesh.dimension==2
464	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
465	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
466	md2.mesh.segments=contourenvelope(md2);
467	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
468	else
469	%First do the connectivity for the contourenvelope in 2d
470	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
471	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
472	md2.mesh.segments=contourenvelope(md2);
473	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
474	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
475	%Then do it for 3d as usual
476	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
477	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
478	end
479
480	%Boundary conditions: Dirichlets on new boundary
481	%Catch the elements that have not been extracted
482	orphans_elem=find(~flag_elem);
483	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
484	%Figure out which node are on the boundary between md2 and md1
485	nodestoflag1=intersect(orphans_node,pos_node);
486	nodestoflag2=Pnode(nodestoflag1);
487	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
488	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
489	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
490	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
491	else
492	md2.stressbalance.spcvx(nodestoflag2)=NaN;
493	md2.stressbalance.spcvy(nodestoflag2)=NaN;
494	disp(' ')
495	disp('!! extract warning: spc values should be checked !!')
496	disp(' ')
497	end
498	%put 0 for vz
499	md2.stressbalance.spcvz(nodestoflag2)=0;
500	end
501	if ~isnan(md1.thermal.spctemperature),
502	md2.thermal.spctemperature(nodestoflag2,1)=1;
503	end
504
505	%Results fields
506	if isstruct(md1.results),
507	md2.results=struct();
508	solutionfields=fields(md1.results);
509	for i=1:length(solutionfields),
510	if isstruct(md1.results.(solutionfields{i}))
511	%get subfields
512	solutionsubfields=fields(md1.results.(solutionfields{i}));
513	for j=1:length(solutionsubfields),
514	field=md1.results.(solutionfields{i}).(solutionsubfields{j});
515	if length(field)==numberofvertices1,
516	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
517	elseif length(field)==numberofelements1,
518	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
519	else
520	md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
521	end
522	end
523	else
524	field=md1.results.(solutionfields{i});
525	if length(field)==numberofvertices1,
526	md2.results.(solutionfields{i})=field(pos_node);
527	elseif length(field)==numberofelements1,
528	md2.results.(solutionfields{i})=field(pos_elem);
529	else
530	md2.results.(solutionfields{i})=field;
531	end
532	end
533	end
534	end
535
536	%Keep track of pos_node and pos_elem
537	md2.mesh.extractedvertices=pos_node;
538	md2.mesh.extractedelements=pos_elem;
539	end % }}}
540	function md = extrude(md,varargin) % {{{
541	%EXTRUDE - vertically extrude a 2d mesh
542	%
543	% vertically extrude a 2d mesh and create corresponding 3d mesh.
544	% The vertical distribution can:
545	% - follow a polynomial law
546	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
547	% - be discribed by a list of coefficients (between 0 and 1)
548	%
549	%
550	% Usage:
551	% md=extrude(md,numlayers,extrusionexponent);
552	% md=extrude(md,numlayers,lowerexponent,upperexponent);
553	% md=extrude(md,listofcoefficients);
554	%
555	% Example:
556	% md=extrude(md,8,3);
557	% md=extrude(md,8,3,2);
558	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
559	%
560	% See also: MODELEXTRACT, COLLAPSE
561
562	%some checks on list of arguments
563	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
564	help extrude;
565	error('extrude error message');
566	end
567
568	%Extrude the mesh
569	if nargin==2, %list of coefficients
570	clist=varargin{1};
571	if any(clist<0) \| any(clist>1),
572	error('extrusioncoefficients must be between 0 and 1');
573	end
574	extrusionlist=sort(unique([clist(:);0;1]));
575	numlayers=length(extrusionlist);
576	elseif nargin==3, %one polynomial law
577	if varargin{2}<=0,
578	help extrude;
579	error('extrusionexponent must be >=0');
580	end
581	numlayers=varargin{1};
582	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
583	elseif nargin==4, %two polynomial laws
584	numlayers=varargin{1};
585	lowerexp=varargin{2};
586	upperexp=varargin{3};
587
588	if varargin{2}<=0 \| varargin{3}<=0,
589	help extrude;
590	error('lower and upper extrusionexponents must be >=0');
591	end
592
593	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
594	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
595	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
596
597	end
598
599	if numlayers<2,
600	error('number of layers should be at least 2');
601	end
602	if md.mesh.dimension==3,
603	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
604	end
605
606	%Initialize with the 2d mesh
607	x3d=[];
608	y3d=[];
609	z3d=[]; %the lower node is on the bed
610	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
611	bed3d=md.geometry.bed;
612
613	%Create the new layers
614	for i=1:numlayers,
615	x3d=[x3d; md.mesh.x];
616	y3d=[y3d; md.mesh.y];
617	%nodes are distributed between bed and surface accordingly to the given exponent
618	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
619	end
620	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
621
622	%Extrude elements
623	elements3d=[];
624	for i=1:numlayers-1,
625	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
626	end
627	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
628
629	%Keep a trace of lower and upper nodes
630	mesh.lowervertex=NaN*ones(number_nodes3d,1);
631	mesh.uppervertex=NaN*ones(number_nodes3d,1);
632	mesh.lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
633	mesh.uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
634	md.mesh.lowervertex=mesh.lowervertex;
635	md.mesh.uppervertex=mesh.uppervertex;
636
637	%same for lower and upper elements
638	mesh.lowerelements=NaN*ones(number_el3d,1);
639	mesh.upperelements=NaN*ones(number_el3d,1);
640	mesh.lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
641	mesh.upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
642	md.mesh.lowerelements=mesh.lowerelements;
643	md.mesh.upperelements=mesh.upperelements;
644
645	%Save old mesh
646	md.mesh.x2d=md.mesh.x;
647	md.mesh.y2d=md.mesh.y;
648	md.mesh.elements2d=md.mesh.elements;
649	md.mesh.numberofelements2d=md.mesh.numberofelements;
650	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
651
652	%Update mesh type
653	md.mesh.dimension=3;
654
655	%Build global 3d mesh
656	md.mesh.elements=elements3d;
657	md.mesh.x=x3d;
658	md.mesh.y=y3d;
659	md.mesh.z=z3d;
660	md.mesh.numberofelements=number_el3d;
661	md.mesh.numberofvertices=number_nodes3d;
662	md.mesh.numberoflayers=numlayers;
663
664	%Ok, now deal with the other fields from the 2d mesh:
665
666	%lat long
667	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
668	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
669
670	%drag coefficient is limited to nodes that are on the bedrock.
671	md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1);
672
673	%p and q (same deal, except for element that are on the bedrock: )
674	md.friction.p=project3d(md,'vector',md.friction.p,'type','element');
675	md.friction.q=project3d(md,'vector',md.friction.q,'type','element');
676
677	%observations
678	md.inversion.vx_obs=project3d(md,'vector',md.inversion.vx_obs,'type','node');
679	md.inversion.vy_obs=project3d(md,'vector',md.inversion.vy_obs,'type','node');
680	md.inversion.vel_obs=project3d(md,'vector',md.inversion.vel_obs,'type','node');
681	md.inversion.thickness_obs=project3d(md,'vector',md.inversion.thickness_obs,'type','node');
682	md.surfaceforcings = extrude(md.surfaceforcings,md);
683	md.balancethickness.thickening_rate=project3d(md,'vector',md.balancethickness.thickening_rate,'type','node');
684
685	%results
686	if ~isnan(md.initialization.vx),md.initialization.vx=project3d(md,'vector',md.initialization.vx,'type','node');end;
687	if ~isnan(md.initialization.vy),md.initialization.vy=project3d(md,'vector',md.initialization.vy,'type','node');end;
688	if ~isnan(md.initialization.vz),md.initialization.vz=project3d(md,'vector',md.initialization.vz,'type','node');end;
689	if ~isnan(md.initialization.vel),md.initialization.vel=project3d(md,'vector',md.initialization.vel,'type','node');end;
690	if ~isnan(md.initialization.temperature),md.initialization.temperature=project3d(md,'vector',md.initialization.temperature,'type','node');end;
691	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project3d(md,'vector',md.initialization.waterfraction,'type','node');end;
692	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project3d(md,'vector',md.initialization.watercolumn,'type','node','layer',1);end;
693	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project3d(md,'vector',md.initialization.sediment_head,'type','node','layer',1);end;
694	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project3d(md,'vector',md.initialization.epl_head,'type','node','layer',1);end;
695
696	%bedinfo and surface info
697	md.mesh.elementonbed=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',1);
698	md.mesh.elementonsurface=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',md.mesh.numberoflayers-1);
699	md.mesh.vertexonbed=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
700	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
701
702	%elementstype
703	if ~isnan(md.flowequation.element_equation)
704	oldelements_type=md.flowequation.element_equation;
705	md.flowequation.element_equation=zeros(number_el3d,1);
706	md.flowequation.element_equation=project3d(md,'vector',oldelements_type,'type','element');
707	end
708
709	%verticestype
710	if ~isnan(md.flowequation.vertex_equation)
711	oldvertices_type=md.flowequation.vertex_equation;
712	md.flowequation.vertex_equation=zeros(number_nodes3d,1);
713	md.flowequation.vertex_equation=project3d(md,'vector',oldvertices_type,'type','node');
714	end
715	md.flowequation.borderSSA=project3d(md,'vector',md.flowequation.borderSSA,'type','node');
716	md.flowequation.borderHO=project3d(md,'vector',md.flowequation.borderHO,'type','node');
717	md.flowequation.borderFS=project3d(md,'vector',md.flowequation.borderFS,'type','node');
718
719	%boundary conditions
720	md.stressbalance.spcvx=project3d(md,'vector',md.stressbalance.spcvx,'type','node');
721	md.stressbalance.spcvy=project3d(md,'vector',md.stressbalance.spcvy,'type','node');
722	md.stressbalance.spcvz=project3d(md,'vector',md.stressbalance.spcvz,'type','node');
723	md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',NaN);
724	md.masstransport.spcthickness=project3d(md,'vector',md.masstransport.spcthickness,'type','node');
725	md.masstransport.calvingrate=project3d(md,'vector',md.masstransport.calvingrate,'type','node');
726	md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
727	md.damage.spcdamage=project3d(md,'vector',md.damage.spcdamage,'type','node');
728	md.stressbalance.referential=project3d(md,'vector',md.stressbalance.referential,'type','node');
729	md.stressbalance.loadingforce=project3d(md,'vector',md.stressbalance.loadingforce,'type','node');
730
731	% Hydrologydc variables
732	if isa(md.hydrology,'hydrologydc');
733	md.hydrology.spcsediment_head=project3d(md,'vector',md.hydrology.spcsediment_head,'type','node','layer',1);
734	md.hydrology.spcepl_head=project3d(md,'vector',md.hydrology.spcepl_head,'type','node','layer',1);
735	md.hydrology.mask_eplactive_node=project3d(md,'vector',md.hydrology.mask_eplactive_node,'type','node','layer',1);
736	md.hydrology.sediment_transmitivity=project3d(md,'vector',md.hydrology.sediment_transmitivity,'type','node','layer',1);
737	md.hydrology.basal_moulin_input=project3d(md,'vector',md.hydrology.basal_moulin_input,'type','node','layer',1);
738	end
739
740	%connectivity
741	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
742	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
743	for i=2:numlayers-1,
744	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
745	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
746	end
747	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
748
749	%materials
750	md.materials.rheology_B=project3d(md,'vector',md.materials.rheology_B,'type','node');
751	md.materials.rheology_n=project3d(md,'vector',md.materials.rheology_n,'type','element');
752
753	%damage
754	md.damage.D=project3d(md,'vector',md.damage.D,'type','node');
755
756	%parameters
757	md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
758	md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
759	md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node');
760	md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node');
761	md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
762	md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
763	md.geometry.bathymetry=project3d(md,'vector',md.geometry.bathymetry,'type','node');
764	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
765	md.mask.groundedice_levelset=project3d(md,'vector',md.mask.groundedice_levelset,'type','node');
766	md.mask.ice_levelset=project3d(md,'vector',md.mask.ice_levelset,'type','node');
767	if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end;
768	if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end;
769	if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end;
770	if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end
771
772	%Put lithostatic pressure if there is an existing pressure
773	if ~isnan(md.initialization.pressure),
774	md.initialization.pressure=md.constants.gmd.materials.rho_ice(md.geometry.surface-md.mesh.z);
775	end
776
777	%special for thermal modeling:
778	md.basalforcings.melting_rate=project3d(md,'vector',md.basalforcings.melting_rate,'type','node','layer',1);
779	if ~isnan(md.basalforcings.geothermalflux)
780	md.basalforcings.geothermalflux=project3d(md,'vector',md.basalforcings.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux
781	end
782
783	%increase connectivity if less than 25:
784	if md.mesh.average_vertex_connectivity<=25,
785	md.mesh.average_vertex_connectivity=100;
786	end
787	end % }}}
788	function md = structtomodel(md,structmd) % {{{
789
790	if ~isstruct(structmd) error('input model is not a structure'); end
791
792	%loaded model is a struct, initialize output and recover all fields
793	md = structtoobj(model,structmd);
794
795	%Old field now classes
796	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
797	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
798
799	%Field name change
800	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
801	if isfield(structmd,'p'), md.friction.p=structmd.p; end
802	if isfield(structmd,'q'), md.friction.q=structmd.p; end
803	if isfield(structmd,'melting'), md.basalforcings.melting_rate=structmd.melting; end
804	if isfield(structmd,'melting_rate'), md.basalforcings.melting_rate=structmd.melting_rate; end
805	if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
806	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
807	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
808	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
809	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
810	if isfield(structmd,'gridonbed'), md.mesh.vertexonbed=structmd.gridonbed; end
811	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
812	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
813	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
814	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
815	if isfield(structmd,'g'), md.constants.g=structmd.g; end
816	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
817	if isfield(structmd,'surface_mass_balance'), md.surfaceforcings.mass_balance=structmd.surface_mass_balance; end
818	if isfield(structmd,'basal_melting_rate'), md.basalforcings.melting_rate=structmd.basal_melting_rate; end
819	if isfield(structmd,'basal_melting_rate_correction'), md.basalforcings.melting_rate_correction=structmd.basal_melting_rate_correction; end
820	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
821	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
822	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
823	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
824	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
825	if isfield(structmd,'riftproperties'), %old implementation
826	md.rifts=rifts();
827	md.rifts.riftproperties=structmd.riftproperties;
828	md.rifts.riftstruct=structmd.rifts;
829	md.rifts.riftproperties=structmd.riftinfo;
830	end
831	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
832	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
833	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
834	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
835	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
836	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
837	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
838	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
839	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
840	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
841	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
842	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
843	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
844	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
845	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
846	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
847	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
848	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
849	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
850	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
851	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
852	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
853	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
854	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
855	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
856	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
857	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
858	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
859	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
860	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
861	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
862	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
863	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
864	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
865	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
866	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
867	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
868	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
869	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
870	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
871	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
872	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
873	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
874	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
875	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
876	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
877	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
878	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
879	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
880	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
881	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
882	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
883	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
884	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
885	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
886	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
887	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
888	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
889	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
890	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
891	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
892	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
893	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
894	if isfield(structmd,'bed'), md.geometry.bed=structmd.bed; end
895	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
896	if isfield(structmd,'bathymetry'), md.geometry.bathymetry=structmd.bathymetry; end
897	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
898	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
899	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
900	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
901	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
902	if isfield(structmd,'hemisphere'), md.mesh.hemisphere=structmd.hemisphere; end
903	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
904	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
905	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
906	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
907	if isfield(structmd,'dim'), md.mesh.dimension=structmd.dim; end
908	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
909	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
910	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
911	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
912	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
913	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
914	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
915	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
916	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
917	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
918	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
919	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
920	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
921	if isfield(structmd,'elementonbed'), md.mesh.elementonbed=structmd.elementonbed; end
922	if isfield(structmd,'elementonsurface'), md.mesh.elementonsurface=structmd.elementonsurface; end
923	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
924	if isfield(structmd,'nodeonbed'), md.mesh.vertexonbed=structmd.nodeonbed; end
925	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
926	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
927	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
928	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
929	if isfield(structmd,'edges'),
930	md.mesh.edges=structmd.edges;
931	md.mesh.edges(isnan(md.mesh.edges))=-1;
932	end
933	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
934	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
935	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
936	if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
937	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
938	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
939	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
940
941	%Field changes
942	if (isfield(structmd,'type') & ischar(structmd.type)),
943	if strcmpi(structmd.type,'2d'), md.mesh.dimension=2; end
944	if strcmpi(structmd.type,'3d'), md.mesh.dimension=3; end
945	end
946	if isnumeric(md.verbose),
947	md.verbose=verbose;
948	end
949
950	if isfield(structmd,'spcvelocity'),
951	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
952	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
953	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
954	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
955	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
956	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
957	end
958	if isfield(structmd,'spcvx'),
959	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
960	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
961	end
962	if isfield(structmd,'spcvy'),
963	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
964	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
965	end
966	if isfield(structmd,'spcvz'),
967	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
968	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
969	end
970	if isfield(structmd,'pressureload'),
971	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
972	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
973	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
974	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
975	end
976	end
977	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
978	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
979	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
980	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
981	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
982	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
983	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
984	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
985	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
986	end
987	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
988	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
989	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
990	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
991	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
992	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
993	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
994	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
995	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
996	end
997	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
998	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
999	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1000	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1001	end
1002	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1003	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1004	if (structmd.groundingline_migration==273), md.groundingline.migration='AgressiveMigration'; end
1005	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1006	end
1007	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1008	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1009	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1010	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1011	end
1012	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1013	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1014	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1015	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1016	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1017	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1018	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1019	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1020	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1021	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1022	end
1023
1024	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1025	md.thermal.stabilization=2;
1026	md.masstransport.stabilization=1;
1027	md.balancethickness.stabilization=1;
1028	end
1029	if isnumeric(md.masstransport.hydrostatic_adjustment)
1030	if md.masstransport.hydrostatic_adjustment==269,
1031	md.masstransport.hydrostatic_adjustment='Incremental';
1032	else
1033	md.masstransport.hydrostatic_adjustment='Absolute';
1034	end
1035	end
1036
1037	%New fields
1038	if ~isfield(structmd,'upperelements');
1039	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1040	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1041	end
1042	if ~isfield(structmd,'lowerelements');
1043	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1044	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1045	end
1046	if ~isfield(structmd,'diagnostic_ref');
1047	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1048	end
1049	if ~isfield(structmd,'loadingforce');
1050	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1051	end
1052
1053	%2013 August 9
1054	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1055	disp('Recovering old prognostic class');
1056	md.masstransport=masstransport(structmd.prognostic);
1057	end
1058	%2013 August 9
1059	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
1060	disp('Recovering old diagnostic class');
1061	md.stressbalance=stressbalance(structmd.diagnostic);
1062	end
1063	end% }}}
1064	function md = setdefaultparameters(md) % {{{
1065
1066	%initialize subclasses
1067	md.mesh = mesh();
1068	md.mask = mask();
1069	md.constants = constants();
1070	md.geometry = geometry();
1071	md.initialization = initialization();
1072	md.surfaceforcings = SMB();
1073	md.basalforcings = basalforcings();
1074	md.friction = friction();
1075	md.rifts = rifts();
1076	md.timestepping = timestepping();
1077	md.groundingline = groundingline();
1078	md.materials = matice();
1079	md.damage = damage();
1080	md.flowequation = flowequation();
1081	md.debug = debug();
1082	md.verbose = verbose();
1083	md.settings = settings();
1084	md.toolkits = toolkits();
1085	md.cluster = generic();
1086	md.balancethickness = balancethickness();
1087	md.stressbalance = stressbalance();
1088	md.hydrology = hydrologyshreve();
1089	md.masstransport = masstransport();
1090	md.thermal = thermal();
1091	md.steadystate = steadystate();
1092	md.transient = transient();
1093	md.gia = gia();
1094	md.autodiff = autodiff();
1095	md.flaim = flaim();
1096	md.inversion = inversion();
1097	md.qmu = qmu();
1098	md.radaroverlay = radaroverlay();
1099	md.results = struct();
1100	md.outputdefinition = outputdefinition();
1101	md.miscellaneous = miscellaneous();
1102	md.private = private();
1103	end
1104	%}}}
1105	function disp(obj) % {{{
1106	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(obj.mesh) ']'],'mesh properties'));
1107	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(obj.mask) ']'],'defines grounded and floating elements'));
1108	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(obj.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1109	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(obj.constants) ']'],'physical constants'));
1110	disp(sprintf('%19s: %-22s -- %s','surfaceforcings' ,['[1x1 ' class(obj.surfaceforcings) ']'],'surface forcings'));
1111	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(obj.basalforcings) ']'],'bed forcings'));
1112	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(obj.materials) ']'],'material properties'));
1113	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(obj.damage) ']'],'parameters for damage evolution solution'));
1114	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(obj.friction) ']'],'basal friction/drag properties'));
1115	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(obj.flowequation) ']'],'flow equations'));
1116	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(obj.timestepping) ']'],'time stepping for transient models'));
1117	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(obj.initialization) ']'],'initial guess/state'));
1118	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(obj.rifts) ']'],'rifts properties'));
1119	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(obj.debug) ']'],'debugging tools (valgrind, gprof)'));
1120	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
1121	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
1122	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(obj.toolkits) ']'],'PETSc options for each solution'));
1123	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
1124	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
1125	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(obj.stressbalance) ']'],'parameters for stressbalance solution'));
1126	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(obj.groundingline) ']'],'parameters for groundingline solution'));
1127	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(obj.hydrology) ']'],'parameters for hydrology solution'));
1128	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(obj.masstransport) ']'],'parameters for masstransport solution'));
1129	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(obj.thermal) ']'],'parameters for thermal solution'));
1130	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
1131	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
1132	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(obj.gia) ']'],'parameters for gia solution'));
1133	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
1134	disp(sprintf('%19s: %-22s -- %s','flaim' ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
1135	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(obj.inversion) ']'],'parameters for inverse methods'));
1136	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(obj.qmu) ']'],'dakota properties'));
1137	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(obj.outputdefinition) ']'],'output definition'));
1138	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(obj.results) ']'],'model results'));
1139	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(obj.radaroverlay) ']'],'radar image for plot overlay'));
1140	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields'));
1141	end % }}}
1142	function memory(obj) % {{{
1143
1144	disp(sprintf('\nMemory imprint:\n'));
1145
1146	fields=properties('model');
1147	mem=0;
1148
1149	for i=1:length(fields),
1150	field=obj.(fields{i});
1151	s=whos('field');
1152	mem=mem+s.bytes/1e6;
1153	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1154	end
1155	disp(sprintf('%19s--%10s','--------------','--------------'));
1156	disp(sprintf('%19s: %g Mb','Total',mem));
1157	end % }}}
1158	function netcdf(obj,filename) % {{{
1159	%NETCDF - save model as netcdf
1160	%
1161	% Usage:
1162	% netcdf(md,filename)
1163	%
1164	% Example:
1165	% netcdf(md,'model.nc');
1166
1167	disp('Saving model as NetCDF');
1168	%1. Create NetCDF file
1169	ncid=netcdf.create(filename,'CLOBBER');
1170	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1171	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' obj.miscellaneous.name ')']);
1172	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1173	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1174
1175	%Preallocate variable id, needed to write variables in netcdf file
1176	var_id=zeros(1000,1);%preallocate
1177
1178	for step=1:2,
1179	counter=0;
1180	[var_id,counter]=structtonc(ncid,'md',obj,0,var_id,counter,step);
1181	if step==1, netcdf.endDef(ncid); end
1182	end
1183
1184	if counter>1000,
1185	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1186	end
1187
1188	netcdf.close(ncid)
1189	end % }}}
1190	function xylim(obj) % {{{
1191
1192	xlim([min(obj.mesh.x) max(obj.mesh.x)]);
1193	ylim([min(obj.mesh.y) max(obj.mesh.y)])
1194	end % }}}
1195	function md=upload(md) % {{{
1196	%the goal of this routine is to upload the model onto a server, and to empty it.
1197	%So first, save the model with a unique name and upload the file to the server:
1198	random_part=fix(rand(1)*10000);
1199	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1200	eval(['save ' id ' md']);
1201
1202	%Now, upload the file:
1203	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1204
1205	%Now, empty this model of everything except settings, and record name of file we just uploaded!
1206	settings_back=md.settings;
1207	md=model();
1208	md.settings=settings_back;
1209	md.settings.upload_filename=id;
1210
1211	%get locally rid of file that was uploaded
1212	eval(['delete ' id]);
1213
1214	end % }}}
1215	function md=download(md) % {{{
1216
1217	%the goal of this routine is to download the internals of the current model from a server, because
1218	%this model is empty, except for the settings which tell us where to go and find this model!
1219
1220	%Download the file:
1221	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1222
1223	name=md.settings.upload_filename;
1224
1225	%Now, load this model:
1226	md=loadmodel(md.settings.upload_filename);
1227
1228	%get locally rid of file that was downloaded
1229	eval(['delete ' name]);
1230
1231	end % }}}
1232	end
1233	end

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