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source: issm/trunk-jpl/src/m/classes/model.m@ 16344

Last change on this file since 16344 was 16344, checked in by cborstad, 11 years ago
BUG: missed project2d for spcdamage
File size: 58.8 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	radaroverlay = 0;
48	miscellaneous = 0;
49	private = 0;
50
51	%}}}
52	end
53	methods (Static)
54	function md = loadobj(md) % {{{
55	% This function is directly called by matlab when a model object is
56	% loaded. If the input is a struct it is an old version of model and
57	% old fields must be recovered (make sure they are in the deprecated
58	% model properties)
59
60	if verLessThan('matlab','7.9'),
61	disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
62	disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
63
64	% This is a Matlab bug: all the fields of md have their default value
65	% Example of error message:
66	% Warning: Error loading an object of class 'model':
67	% Undefined function or method 'exist' for input arguments of type 'cell'
68	%
69	% This has been fixed in MATLAB 7.9 (R2009b) and later versions
70	end
71
72	if isstruct(md)
73	disp('Recovering model object from a previous version');
74	md = structtomodel(model,md);
75	end
76
77	%2012 August 4th
78	if isa(md.materials,'materials'),
79	disp('Recovering old materials');
80	if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
81	md.materials=matice(md.materials);
82	else
83	md.materials=matdamageice(md.materials);
84	end
85	end
86	%2013 April 12
87	if numel(md.stressbalance.loadingforce==1)
88	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
89	end
90	%2013 April 17
91	if isa(md.hydrology,'hydrology'),
92	disp('Recovering old hydrology class');
93	md.hydrology=hydrologyshreve(md.materials);
94	end
95	end% }}}
96	end
97	methods
98	function md = model(varargin) % {{{
99
100	switch nargin
101	case 0
102	md=setdefaultparameters(md);
103	otherwise
104	error('model constructor error message: 0 of 1 argument only in input.');
105	end
106	end
107	%}}}
108	function md = checkmessage(md,string) % {{{
109	if(nargout~=1) error('wrong usage, model must be an output'); end
110	disp(['model not consistent: ' string]);
111	md.private.isconsistent=false;
112	end
113	%}}}
114	function md = collapse(md)% {{{
115	%COLLAPSE - collapses a 3d mesh into a 2d mesh
116	%
117	% This routine collapses a 3d model into a 2d model
118	% and collapses all the fileds of the 3d model by
119	% taking their depth-averaged values
120	%
121	% Usage:
122	% md=collapse(md)
123	%
124	% See also: EXTRUDE, MODELEXTRACT
125
126	%Check that the model is really a 3d model
127	if ~md.mesh.dimension==3,
128	error('collapse error message: only 3d mesh can be collapsed')
129	end
130
131	%Start with changing alle the fields from the 3d mesh
132
133	%drag is limited to nodes that are on the bedrock.
134	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
135
136	%p and q (same deal, except for element that are on the bedrock: )
137	md.friction.p=project2d(md,md.friction.p,1);
138	md.friction.q=project2d(md,md.friction.q,1);
139
140	%observations
141	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
142	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
143	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
144	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
145	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
146	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
147	if ~isnan(md.surfaceforcings.mass_balance),
148	md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers);
149	end;
150	if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
151
152	%results
153	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
154	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
155	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
156	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
157	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
158
159	%gia
160	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
161	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
162
163	%bedinfo and surface info
164	md.mesh.elementonbed=ones(md.mesh.numberofelements2d,1);
165	md.mesh.elementonsurface=ones(md.mesh.numberofelements2d,1);
166	md.mesh.vertexonbed=ones(md.mesh.numberofvertices2d,1);
167	md.mesh.vertexonsurface=ones(md.mesh.numberofvertices2d,1);
168
169	%elementstype
170	if ~isnan(md.flowequation.element_equation)
171	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
172	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
173	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
174	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
175	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
176	end
177
178	%boundary conditions
179	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
180	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
181	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
182	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
183	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
184	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
185	md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers)
186	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
187
188	%materials
189	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
190	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
191
192	%damage:
193	md.damage.D=DepthAverage(md,md.damage.D);
194
195	%special for thermal modeling:
196	md.basalforcings.melting_rate=project2d(md,md.basalforcings.melting_rate,1);
197	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
198
199	%update of connectivity matrix
200	md.mesh.average_vertex_connectivity=25;
201
202	%Collapse the mesh
203	nodes2d=md.mesh.numberofvertices2d;
204	elements2d=md.mesh.numberofelements2d;
205
206	%parameters
207	md.geometry.surface=project2d(md,md.geometry.surface,1);
208	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
209	md.geometry.bed=project2d(md,md.geometry.bed,1);
210	md.geometry.bathymetry=project2d(md,md.geometry.bathymetry,1);
211	md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
212	md.mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
213	md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
214	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
215
216	%lat long
217	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
218	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
219
220	%Initialize with the 2d mesh
221	md.mesh.x=md.mesh.x2d;
222	md.mesh.y=md.mesh.y2d;
223	md.mesh.z=zeros(size(md.mesh.x2d));
224	md.mesh.numberofvertices=md.mesh.numberofvertices2d;
225	md.mesh.numberofelements=md.mesh.numberofelements2d;
226	md.mesh.elements=md.mesh.elements2d;
227
228	%Keep a trace of lower and upper nodes
229	md.mesh.lowervertex=NaN;
230	md.mesh.uppervertex=NaN;
231	md.mesh.lowerelements=NaN;
232	md.mesh.upperelements=NaN;
233
234	%Remove old mesh
235	md.mesh.x2d=NaN;
236	md.mesh.y2d=NaN;
237	md.mesh.elements2d=NaN;
238	md.mesh.numberofelements2d=md.mesh.numberofelements;
239	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
240	md.mesh.numberoflayers=0;
241
242	%Update mesh type
243	md.mesh.dimension=2;
244	end % }}}
245	function md2 = extract(md,area) % {{{
246	%extract - extract a model according to an Argus contour or flag list
247	%
248	% This routine extracts a submodel from a bigger model with respect to a given contour
249	% md must be followed by the corresponding exp file or flags list
250	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
251	% If user wants every element outside the domain to be
252	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
253	% an empty string '' will be considered as an empty domain
254	% a string 'all' will be considered as the entire domain
255	%
256	% Usage:
257	% md2=extract(md,area);
258	%
259	% Examples:
260	% md2=extract(md,'Domain.exp');
261	%
262	% See also: EXTRUDE, COLLAPSE
263
264	%copy model
265	md1=md;
266
267	%some checks
268	if ((nargin~=2) \| (nargout~=1)),
269	help extract
270	error('extract error message: bad usage');
271	end
272
273	%get elements that are inside area
274	flag_elem=FlagElements(md1,area);
275	if ~any(flag_elem),
276	error('extracted model is empty');
277	end
278
279	%kick out all elements with 3 dirichlets
280	spc_elem=find(~flag_elem);
281	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
282	flag=ones(md1.mesh.numberofvertices,1);
283	flag(spc_node)=0;
284	pos=find(sum(flag(md1.mesh.elements),2)==0);
285	flag_elem(pos)=0;
286
287	%extracted elements and nodes lists
288	pos_elem=find(flag_elem);
289	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
290
291	%keep track of some fields
292	numberofvertices1=md1.mesh.numberofvertices;
293	numberofelements1=md1.mesh.numberofelements;
294	numberofvertices2=length(pos_node);
295	numberofelements2=length(pos_elem);
296	flag_node=zeros(numberofvertices1,1);
297	flag_node(pos_node)=1;
298
299	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
300	Pelem=zeros(numberofelements1,1);
301	Pelem(pos_elem)=[1:numberofelements2]';
302	Pnode=zeros(numberofvertices1,1);
303	Pnode(pos_node)=[1:numberofvertices2]';
304
305	%renumber the elements (some nodes won't exist anymore)
306	elements_1=md1.mesh.elements;
307	elements_2=elements_1(pos_elem,:);
308	elements_2(:,1)=Pnode(elements_2(:,1));
309	elements_2(:,2)=Pnode(elements_2(:,2));
310	elements_2(:,3)=Pnode(elements_2(:,3));
311	if md1.mesh.dimension==3,
312	elements_2(:,4)=Pnode(elements_2(:,4));
313	elements_2(:,5)=Pnode(elements_2(:,5));
314	elements_2(:,6)=Pnode(elements_2(:,6));
315	end
316
317	%OK, now create the new model!
318
319	%take every field from model
320	md2=md1;
321
322	%automatically modify fields
323
324	%loop over model fields
325	model_fields=fields(md1);
326	for i=1:length(model_fields),
327	%get field
328	field=md1.(model_fields{i});
329	fieldsize=size(field);
330	if isobject(field), %recursive call
331	object_fields=fields(md1.(model_fields{i}));
332	for j=1:length(object_fields),
333	%get field
334	field=md1.(model_fields{i}).(object_fields{j});
335	fieldsize=size(field);
336	%size = number of nodes * n
337	if fieldsize(1)==numberofvertices1
338	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
339	elseif (fieldsize(1)==numberofvertices1+1)
340	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
341	%size = number of elements * n
342	elseif fieldsize(1)==numberofelements1
343	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
344	end
345	end
346	else
347	%size = number of nodes * n
348	if fieldsize(1)==numberofvertices1
349	md2.(model_fields{i})=field(pos_node,:);
350	elseif (fieldsize(1)==numberofvertices1+1)
351	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
352	%size = number of elements * n
353	elseif fieldsize(1)==numberofelements1
354	md2.(model_fields{i})=field(pos_elem,:);
355	end
356	end
357	end
358
359	%modify some specific fields
360
361	%Mesh
362	md2.mesh.numberofelements=numberofelements2;
363	md2.mesh.numberofvertices=numberofvertices2;
364	md2.mesh.elements=elements_2;
365
366	%mesh.uppervertex mesh.lowervertex
367	if md1.mesh.dimension==3
368	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
369	pos=find(~isnan(md2.mesh.uppervertex));
370	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
371
372	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
373	pos=find(~isnan(md2.mesh.lowervertex));
374	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
375
376	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
377	pos=find(~isnan(md2.mesh.upperelements));
378	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
379
380	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
381	pos=find(~isnan(md2.mesh.lowerelements));
382	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
383	end
384
385	%Initial 2d mesh
386	if md1.mesh.dimension==3
387	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
388	pos_elem_2d=find(flag_elem_2d);
389	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
390	pos_node_2d=find(flag_node_2d);
391
392	md2.mesh.numberofelements2d=length(pos_elem_2d);
393	md2.mesh.numberofvertices2d=length(pos_node_2d);
394	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
395	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
396	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
397	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
398
399	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
400	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
401	end
402
403	%Edges
404	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
405	%renumber first two columns
406	pos=find(md2.mesh.edges(:,4)~=-1);
407	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
408	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
409	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
410	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
411	%remove edges when the 2 vertices are not in the domain.
412	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
413	%Replace all zeros by -1 in the last two columns
414	pos=find(md2.mesh.edges(:,3)==0);
415	md2.mesh.edges(pos,3)=-1;
416	pos=find(md2.mesh.edges(:,4)==0);
417	md2.mesh.edges(pos,4)=-1;
418	%Invert -1 on the third column with last column (Also invert first two columns!!)
419	pos=find(md2.mesh.edges(:,3)==-1);
420	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
421	md2.mesh.edges(pos,4)=-1;
422	values=md2.mesh.edges(pos,2);
423	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
424	md2.mesh.edges(pos,1)=values;
425	%Finally remove edges that do not belong to any element
426	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
427	md2.mesh.edges(pos,:)=[];
428	end
429
430	%Penalties
431	if ~isnan(md2.stressbalance.vertex_pairing),
432	for i=1:size(md1.stressbalance.vertex_pairing,1);
433	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
434	end
435	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
436	end
437	if ~isnan(md2.masstransport.vertex_pairing),
438	for i=1:size(md1.masstransport.vertex_pairing,1);
439	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
440	end
441	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
442	end
443
444	%recreate segments
445	if md1.mesh.dimension==2
446	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
447	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
448	md2.mesh.segments=contourenvelope(md2);
449	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
450	else
451	%First do the connectivity for the contourenvelope in 2d
452	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
453	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
454	md2.mesh.segments=contourenvelope(md2);
455	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
456	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
457	%Then do it for 3d as usual
458	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
459	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
460	end
461
462	%Boundary conditions: Dirichlets on new boundary
463	%Catch the elements that have not been extracted
464	orphans_elem=find(~flag_elem);
465	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
466	%Figure out which node are on the boundary between md2 and md1
467	nodestoflag1=intersect(orphans_node,pos_node);
468	nodestoflag2=Pnode(nodestoflag1);
469	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
470	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
471	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
472	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
473	else
474	md2.stressbalance.spcvx(nodestoflag2)=NaN;
475	md2.stressbalance.spcvy(nodestoflag2)=NaN;
476	disp(' ')
477	disp('!! extract warning: spc values should be checked !!')
478	disp(' ')
479	end
480	%put 0 for vz
481	md2.stressbalance.spcvz(nodestoflag2)=0;
482	end
483	if ~isnan(md1.thermal.spctemperature),
484	md2.thermal.spctemperature(nodestoflag2,1)=1;
485	end
486
487	%Results fields
488	if isstruct(md1.results),
489	md2.results=struct();
490	solutionfields=fields(md1.results);
491	for i=1:length(solutionfields),
492	if isstruct(md1.results.(solutionfields{i}))
493	%get subfields
494	solutionsubfields=fields(md1.results.(solutionfields{i}));
495	for j=1:length(solutionsubfields),
496	field=md1.results.(solutionfields{i}).(solutionsubfields{j});
497	if length(field)==numberofvertices1,
498	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
499	elseif length(field)==numberofelements1,
500	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
501	else
502	md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
503	end
504	end
505	else
506	field=md1.results.(solutionfields{i});
507	if length(field)==numberofvertices1,
508	md2.results.(solutionfields{i})=field(pos_node);
509	elseif length(field)==numberofelements1,
510	md2.results.(solutionfields{i})=field(pos_elem);
511	else
512	md2.results.(solutionfields{i})=field;
513	end
514	end
515	end
516	end
517
518	%Keep track of pos_node and pos_elem
519	md2.mesh.extractedvertices=pos_node;
520	md2.mesh.extractedelements=pos_elem;
521	end % }}}
522	function md = extrude(md,varargin) % {{{
523	%EXTRUDE - vertically extrude a 2d mesh
524	%
525	% vertically extrude a 2d mesh and create corresponding 3d mesh.
526	% The vertical distribution can:
527	% - follow a polynomial law
528	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
529	% - be discribed by a list of coefficients (between 0 and 1)
530	%
531	%
532	% Usage:
533	% md=extrude(md,numlayers,extrusionexponent);
534	% md=extrude(md,numlayers,lowerexponent,upperexponent);
535	% md=extrude(md,listofcoefficients);
536	%
537	% Example:
538	% md=extrude(md,8,3);
539	% md=extrude(md,8,3,2);
540	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
541	%
542	% See also: MODELEXTRACT, COLLAPSE
543
544	%some checks on list of arguments
545	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
546	help extrude;
547	error('extrude error message');
548	end
549
550	%Extrude the mesh
551	if nargin==2, %list of coefficients
552	clist=varargin{1};
553	if any(clist<0) \| any(clist>1),
554	error('extrusioncoefficients must be between 0 and 1');
555	end
556	extrusionlist=sort(unique([clist(:);0;1]));
557	numlayers=length(extrusionlist);
558	elseif nargin==3, %one polynomial law
559	if varargin{2}<=0,
560	help extrude;
561	error('extrusionexponent must be >=0');
562	end
563	numlayers=varargin{1};
564	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
565	elseif nargin==4, %two polynomial laws
566	numlayers=varargin{1};
567	lowerexp=varargin{2};
568	upperexp=varargin{3};
569
570	if varargin{2}<=0 \| varargin{3}<=0,
571	help extrude;
572	error('lower and upper extrusionexponents must be >=0');
573	end
574
575	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
576	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
577	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
578
579	end
580
581	if numlayers<2,
582	error('number of layers should be at least 2');
583	end
584	if md.mesh.dimension==3,
585	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
586	end
587
588	%Initialize with the 2d mesh
589	x3d=[];
590	y3d=[];
591	z3d=[]; %the lower node is on the bed
592	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
593	bed3d=md.geometry.bed;
594
595	%Create the new layers
596	for i=1:numlayers,
597	x3d=[x3d; md.mesh.x];
598	y3d=[y3d; md.mesh.y];
599	%nodes are distributed between bed and surface accordingly to the given exponent
600	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
601	end
602	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
603
604	%Extrude elements
605	elements3d=[];
606	for i=1:numlayers-1,
607	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
608	end
609	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
610
611	%Keep a trace of lower and upper nodes
612	mesh.lowervertex=NaN*ones(number_nodes3d,1);
613	mesh.uppervertex=NaN*ones(number_nodes3d,1);
614	mesh.lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
615	mesh.uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
616	md.mesh.lowervertex=mesh.lowervertex;
617	md.mesh.uppervertex=mesh.uppervertex;
618
619	%same for lower and upper elements
620	mesh.lowerelements=NaN*ones(number_el3d,1);
621	mesh.upperelements=NaN*ones(number_el3d,1);
622	mesh.lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
623	mesh.upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
624	md.mesh.lowerelements=mesh.lowerelements;
625	md.mesh.upperelements=mesh.upperelements;
626
627	%Save old mesh
628	md.mesh.x2d=md.mesh.x;
629	md.mesh.y2d=md.mesh.y;
630	md.mesh.elements2d=md.mesh.elements;
631	md.mesh.numberofelements2d=md.mesh.numberofelements;
632	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
633
634	%Update mesh type
635	md.mesh.dimension=3;
636
637	%Build global 3d mesh
638	md.mesh.elements=elements3d;
639	md.mesh.x=x3d;
640	md.mesh.y=y3d;
641	md.mesh.z=z3d;
642	md.mesh.numberofelements=number_el3d;
643	md.mesh.numberofvertices=number_nodes3d;
644	md.mesh.numberoflayers=numlayers;
645
646	%Ok, now deal with the other fields from the 2d mesh:
647
648	%lat long
649	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
650	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
651
652	%drag coefficient is limited to nodes that are on the bedrock.
653	md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1);
654
655	%p and q (same deal, except for element that are on the bedrock: )
656	md.friction.p=project3d(md,'vector',md.friction.p,'type','element');
657	md.friction.q=project3d(md,'vector',md.friction.q,'type','element');
658
659	%observations
660	md.inversion.vx_obs=project3d(md,'vector',md.inversion.vx_obs,'type','node');
661	md.inversion.vy_obs=project3d(md,'vector',md.inversion.vy_obs,'type','node');
662	md.inversion.vel_obs=project3d(md,'vector',md.inversion.vel_obs,'type','node');
663	md.surfaceforcings.mass_balance=project3d(md,'vector',md.surfaceforcings.mass_balance,'type','node');
664	md.surfaceforcings.precipitation=project3d(md,'vector',md.surfaceforcings.precipitation,'type','node');
665	md.balancethickness.thickening_rate=project3d(md,'vector',md.balancethickness.thickening_rate,'type','node');
666	md.surfaceforcings.monthlytemperatures=project3d(md,'vector',md.surfaceforcings.monthlytemperatures,'type','node');
667
668	%results
669	if ~isnan(md.initialization.vx),md.initialization.vx=project3d(md,'vector',md.initialization.vx,'type','node');end;
670	if ~isnan(md.initialization.vy),md.initialization.vy=project3d(md,'vector',md.initialization.vy,'type','node');end;
671	if ~isnan(md.initialization.vz),md.initialization.vz=project3d(md,'vector',md.initialization.vz,'type','node');end;
672	if ~isnan(md.initialization.vel),md.initialization.vel=project3d(md,'vector',md.initialization.vel,'type','node');end;
673	if ~isnan(md.initialization.temperature),md.initialization.temperature=project3d(md,'vector',md.initialization.temperature,'type','node');end;
674	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project3d(md,'vector',md.initialization.waterfraction,'type','node');end;
675	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project3d(md,'vector',md.initialization.watercolumn,'type','node','layer',1);end;
676
677	%bedinfo and surface info
678	md.mesh.elementonbed=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',1);
679	md.mesh.elementonsurface=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',md.mesh.numberoflayers-1);
680	md.mesh.vertexonbed=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
681	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
682
683	%elementstype
684	if ~isnan(md.flowequation.element_equation)
685	oldelements_type=md.flowequation.element_equation;
686	md.flowequation.element_equation=zeros(number_el3d,1);
687	md.flowequation.element_equation=project3d(md,'vector',oldelements_type,'type','element');
688	end
689
690	%verticestype
691	if ~isnan(md.flowequation.vertex_equation)
692	oldvertices_type=md.flowequation.vertex_equation;
693	md.flowequation.vertex_equation=zeros(number_nodes3d,1);
694	md.flowequation.vertex_equation=project3d(md,'vector',oldvertices_type,'type','node');
695	end
696	md.flowequation.borderSSA=project3d(md,'vector',md.flowequation.borderSSA,'type','node');
697	md.flowequation.borderHO=project3d(md,'vector',md.flowequation.borderHO,'type','node');
698	md.flowequation.borderFS=project3d(md,'vector',md.flowequation.borderFS,'type','node');
699
700	%boundary conditions
701	md.stressbalance.spcvx=project3d(md,'vector',md.stressbalance.spcvx,'type','node');
702	md.stressbalance.spcvy=project3d(md,'vector',md.stressbalance.spcvy,'type','node');
703	md.stressbalance.spcvz=project3d(md,'vector',md.stressbalance.spcvz,'type','node');
704	md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',NaN);
705	md.masstransport.spcthickness=project3d(md,'vector',md.masstransport.spcthickness,'type','node');
706	md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
707	md.damage.spcdamage=project3d(md,'vector',md.damage.spcdamage,'type','node');
708	md.stressbalance.referential=project3d(md,'vector',md.stressbalance.referential,'type','node');
709	md.stressbalance.loadingforce=project3d(md,'vector',md.stressbalance.loadingforce,'type','node');
710
711	%connectivity
712	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
713	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
714	for i=2:numlayers-1,
715	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
716	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
717	end
718	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
719
720	%materials
721	md.materials.rheology_B=project3d(md,'vector',md.materials.rheology_B,'type','node');
722	md.materials.rheology_n=project3d(md,'vector',md.materials.rheology_n,'type','element');
723
724	%damage
725	md.damage.D=project3d(md,'vector',md.damage.D,'type','node');
726
727	%parameters
728	md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
729	md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
730	md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node');
731	md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node');
732	md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
733	md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
734	md.geometry.bathymetry=project3d(md,'vector',md.geometry.bathymetry,'type','node');
735	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
736	md.mask.groundedice_levelset=project3d(md,'vector',md.mask.groundedice_levelset,'type','node');
737	md.mask.ice_levelset=project3d(md,'vector',md.mask.ice_levelset,'type','node');
738	if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end;
739	if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end;
740	if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end;
741	if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end
742	if(md.surfaceforcings.isdelta18o),md.surfaceforcings.temperatures_lgm=project3d(md,'vector',md.surfaceforcings.temperatures_lgm,'type','node');end
743	if(md.surfaceforcings.isdelta18o),md.surfaceforcings.temperatures_presentday=project3d(md,'vector',md.surfaceforcings.temperatures_presentday,'type','node');end
744	if(md.surfaceforcings.isdelta18o),md.surfaceforcings.precipitations_presentday=project3d(md,'vector',md.surfaceforcings.precipitations_presentday,'type','node');end
745
746	%Put lithostatic pressure if there is an existing pressure
747	if ~isnan(md.initialization.pressure),
748	md.initialization.pressure=md.constants.gmd.materials.rho_ice(md.geometry.surface-md.mesh.z);
749	end
750
751	%special for thermal modeling:
752	md.basalforcings.melting_rate=project3d(md,'vector',md.basalforcings.melting_rate,'type','node','layer',1);
753	if ~isnan(md.basalforcings.geothermalflux)
754	md.basalforcings.geothermalflux=project3d(md,'vector',md.basalforcings.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux
755	end
756
757	%increase connectivity if less than 25:
758	if md.mesh.average_vertex_connectivity<=25,
759	md.mesh.average_vertex_connectivity=100;
760	end
761	end % }}}
762	function md = structtomodel(md,structmd) % {{{
763
764	if ~isstruct(structmd) error('input model is not a structure'); end
765
766	%loaded model is a struct, initialize output and recover all fields
767	md = structtoobj(model,structmd);
768
769	%Old field now classes
770	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
771	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
772
773	%Field name change
774	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
775	if isfield(structmd,'p'), md.friction.p=structmd.p; end
776	if isfield(structmd,'q'), md.friction.q=structmd.p; end
777	if isfield(structmd,'melting'), md.basalforcings.melting_rate=structmd.melting; end
778	if isfield(structmd,'melting_rate'), md.basalforcings.melting_rate=structmd.melting_rate; end
779	if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
780	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
781	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
782	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
783	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
784	if isfield(structmd,'gridonbed'), md.mesh.vertexonbed=structmd.gridonbed; end
785	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
786	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
787	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
788	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
789	if isfield(structmd,'g'), md.constants.g=structmd.g; end
790	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
791	if isfield(structmd,'surface_mass_balance'), md.surfaceforcings.mass_balance=structmd.surface_mass_balance; end
792	if isfield(structmd,'basal_melting_rate'), md.basalforcings.melting_rate=structmd.basal_melting_rate; end
793	if isfield(structmd,'basal_melting_rate_correction'), md.basalforcings.melting_rate_correction=structmd.basal_melting_rate_correction; end
794	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
795	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
796	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
797	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
798	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
799	if isfield(structmd,'riftproperties'), %old implementation
800	md.rifts=rifts();
801	md.rifts.riftproperties=structmd.riftproperties;
802	md.rifts.riftstruct=structmd.rifts;
803	md.rifts.riftproperties=structmd.riftinfo;
804	end
805	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
806	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
807	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
808	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
809	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
810	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
811	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
812	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
813	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
814	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
815	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
816	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
817	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
818	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
819	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
820	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
821	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
822	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
823	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
824	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
825	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
826	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
827	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
828	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
829	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
830	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
831	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
832	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
833	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
834	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
835	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
836	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
837	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
838	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
839	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
840	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
841	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
842	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
843	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
844	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
845	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
846	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
847	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
848	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
849	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
850	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
851	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
852	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
853	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
854	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
855	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
856	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
857	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
858	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
859	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
860	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
861	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
862	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
863	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
864	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
865	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
866	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
867	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
868	if isfield(structmd,'bed'), md.geometry.bed=structmd.bed; end
869	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
870	if isfield(structmd,'bathymetry'), md.geometry.bathymetry=structmd.bathymetry; end
871	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
872	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
873	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
874	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
875	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
876	if isfield(structmd,'hemisphere'), md.mesh.hemisphere=structmd.hemisphere; end
877	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
878	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
879	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
880	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
881	if isfield(structmd,'dim'), md.mesh.dimension=structmd.dim; end
882	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
883	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
884	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
885	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
886	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
887	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
888	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
889	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
890	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
891	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
892	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
893	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
894	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
895	if isfield(structmd,'elementonbed'), md.mesh.elementonbed=structmd.elementonbed; end
896	if isfield(structmd,'elementonsurface'), md.mesh.elementonsurface=structmd.elementonsurface; end
897	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
898	if isfield(structmd,'nodeonbed'), md.mesh.vertexonbed=structmd.nodeonbed; end
899	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
900	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
901	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
902	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
903	if isfield(structmd,'edges'),
904	md.mesh.edges=structmd.edges;
905	md.mesh.edges(isnan(md.mesh.edges))=-1;
906	end
907	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
908	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
909	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
910	if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
911	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
912	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
913	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
914
915	%Field changes
916	if (isfield(structmd,'type') & ischar(structmd.type)),
917	if strcmpi(structmd.type,'2d'), md.mesh.dimension=2; end
918	if strcmpi(structmd.type,'3d'), md.mesh.dimension=3; end
919	end
920	if isnumeric(md.verbose),
921	md.verbose=verbose;
922	end
923
924	if isfield(structmd,'spcvelocity'),
925	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
926	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
927	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
928	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
929	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
930	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
931	end
932	if isfield(structmd,'spcvx'),
933	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
934	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
935	end
936	if isfield(structmd,'spcvy'),
937	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
938	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
939	end
940	if isfield(structmd,'spcvz'),
941	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
942	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
943	end
944	if isfield(structmd,'pressureload'),
945	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
946	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
947	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
948	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
949	end
950	end
951	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
952	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
953	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
954	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
955	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
956	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
957	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
958	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
959	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
960	end
961	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
962	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
963	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
964	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
965	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
966	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
967	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
968	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
969	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
970	end
971	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
972	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
973	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
974	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
975	end
976	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
977	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
978	if (structmd.groundingline_migration==273), md.groundingline.migration='AgressiveMigration'; end
979	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
980	end
981	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
982	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
983	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
984	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
985	end
986	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
987	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
988	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
989	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
990	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
991	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
992	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
993	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
994	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
995	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
996	end
997
998	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
999	md.thermal.stabilization=2;
1000	md.masstransport.stabilization=1;
1001	md.balancethickness.stabilization=1;
1002	end
1003	if isnumeric(md.masstransport.hydrostatic_adjustment)
1004	if md.masstransport.hydrostatic_adjustment==269,
1005	md.masstransport.hydrostatic_adjustment='Incremental';
1006	else
1007	md.masstransport.hydrostatic_adjustment='Absolute';
1008	end
1009	end
1010
1011	%New fields
1012	if ~isfield(structmd,'upperelements');
1013	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1014	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1015	end
1016	if ~isfield(structmd,'lowerelements');
1017	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1018	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1019	end
1020	if ~isfield(structmd,'diagnostic_ref');
1021	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1022	end
1023	if ~isfield(structmd,'loadingforce');
1024	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1025	end
1026
1027	%2013 August 9
1028	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1029	disp('Recovering old prognostic class');
1030	md.masstransport=masstransport(structmd.prognostic);
1031	end
1032	%2013 August 9
1033	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
1034	disp('Recovering old diagnostic class');
1035	md.stressbalance=stressbalance(structmd.diagnostic);
1036	end
1037	end% }}}
1038	function md = setdefaultparameters(md) % {{{
1039
1040	%initialize subclasses
1041	md.mesh = mesh();
1042	md.mask = mask();
1043	md.constants = constants();
1044	md.geometry = geometry();
1045	md.initialization = initialization();
1046	md.surfaceforcings = surfaceforcings();
1047	md.basalforcings = basalforcings();
1048	md.friction = friction();
1049	md.rifts = rifts();
1050	md.timestepping = timestepping();
1051	md.groundingline = groundingline();
1052	md.materials = matice();
1053	md.damage = damage();
1054	md.flowequation = flowequation();
1055	md.debug = debug();
1056	md.verbose = verbose();
1057	md.settings = settings();
1058	md.toolkits = toolkits();
1059	md.cluster = generic();
1060	md.balancethickness = balancethickness();
1061	md.stressbalance = stressbalance();
1062	md.hydrology = hydrologyshreve();
1063	md.masstransport = masstransport();
1064	md.thermal = thermal();
1065	md.steadystate = steadystate();
1066	md.transient = transient();
1067	md.gia = gia();
1068	md.autodiff = autodiff();
1069	md.flaim = flaim();
1070	md.inversion = inversion();
1071	md.qmu = qmu();
1072	md.radaroverlay = radaroverlay();
1073	md.results = struct();
1074	md.miscellaneous = miscellaneous();
1075	md.private = private();
1076	end
1077	%}}}
1078	function disp(obj) % {{{
1079	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(obj.mesh) ']'],'mesh properties'));
1080	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(obj.mask) ']'],'defines grounded and floating elements'));
1081	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(obj.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1082	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(obj.constants) ']'],'physical constants'));
1083	disp(sprintf('%19s: %-22s -- %s','surfaceforcings' ,['[1x1 ' class(obj.surfaceforcings) ']'],'surface forcings'));
1084	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(obj.basalforcings) ']'],'bed forcings'));
1085	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(obj.materials) ']'],'material properties'));
1086	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(obj.damage) ']'],'damage propagation laws'));
1087	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(obj.friction) ']'],'basal friction/drag properties'));
1088	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(obj.flowequation) ']'],'flow equations'));
1089	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(obj.timestepping) ']'],'time stepping for transient models'));
1090	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(obj.initialization) ']'],'initial guess/state'));
1091	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(obj.rifts) ']'],'rifts properties'));
1092	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(obj.debug) ']'],'debugging tools (valgrind, gprof)'));
1093	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
1094	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
1095	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(obj.toolkits) ']'],'PETSc options for each solution'));
1096	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
1097	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
1098	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(obj.stressbalance) ']'],'parameters for stressbalance solution'));
1099	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(obj.groundingline) ']'],'parameters for groundingline solution'));
1100	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(obj.hydrology) ']'],'parameters for hydrology solution'));
1101	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(obj.masstransport) ']'],'parameters for masstransport solution'));
1102	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(obj.thermal) ']'],'parameters for thermal solution'));
1103	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
1104	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
1105	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(obj.gia) ']'],'parameters for gia solution'));
1106	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
1107	disp(sprintf('%19s: %-22s -- %s','flaim' ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
1108	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(obj.inversion) ']'],'parameters for inverse methods'));
1109	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(obj.qmu) ']'],'dakota properties'));
1110	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(obj.results) ']'],'model results'));
1111	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(obj.radaroverlay) ']'],'radar image for plot overlay'));
1112	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields'));
1113	end % }}}
1114	function memory(obj) % {{{
1115
1116	disp(sprintf('\nMemory imprint:\n'));
1117
1118	fields=properties('model');
1119	mem=0;
1120
1121	for i=1:length(fields),
1122	field=obj.(fields{i});
1123	s=whos('field');
1124	mem=mem+s.bytes/1e6;
1125	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1126	end
1127	disp(sprintf('%19s--%10s','--------------','--------------'));
1128	disp(sprintf('%19s: %g Mb','Total',mem));
1129	end % }}}
1130	function netcdf(obj,filename) % {{{
1131	%NETCDF - save model as netcdf
1132	%
1133	% Usage:
1134	% netcdf(md,filename)
1135	%
1136	% Example:
1137	% netcdf(md,'model.nc');
1138
1139	disp('Saving model as NetCDF');
1140	%1. Create NetCDF file
1141	ncid=netcdf.create(filename,'CLOBBER');
1142	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1143	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' obj.miscellaneous.name ')']);
1144	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1145	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1146
1147	%Preallocate variable id, needed to write variables in netcdf file
1148	var_id=zeros(1000,1);%preallocate
1149
1150	for step=1:2,
1151	counter=0;
1152	[var_id,counter]=structtonc(ncid,'md',obj,0,var_id,counter,step);
1153	if step==1, netcdf.endDef(ncid); end
1154	end
1155
1156	if counter>1000,
1157	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1158	end
1159
1160	netcdf.close(ncid)
1161	end % }}}
1162	function xylim(obj) % {{{
1163
1164	xlim([min(obj.mesh.x) max(obj.mesh.x)]);
1165	ylim([min(obj.mesh.y) max(obj.mesh.y)])
1166	end % }}}
1167	function md=upload(md) % {{{
1168	%the goal of this routine is to upload the model onto a server, and to empty it.
1169	%So first, save the model with a unique name and upload the file to the server:
1170	random_part=fix(rand(1)*10000);
1171	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1172	eval(['save ' id ' md']);
1173
1174	%Now, upload the file:
1175	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1176
1177	%Now, empty this model of everything except settings, and record name of file we just uploaded!
1178	settings_back=md.settings;
1179	md=model();
1180	md.settings=settings_back;
1181	md.settings.upload_filename=id;
1182
1183	%get locally rid of file that was uploaded
1184	eval(['delete ' id]);
1185
1186	end % }}}
1187	function md=download(md) % {{{
1188
1189	%the goal of this routine is to download the internals of the current model from a server, because
1190	%this model is empty, except for the settings which tell us where to go and find this model!
1191
1192	%Download the file:
1193	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1194
1195	name=md.settings.upload_filename;
1196
1197	%Now, load this model:
1198	md=loadmodel(md.settings.upload_filename);
1199
1200	%get locally rid of file that was downloaded
1201	eval(['delete ' name]);
1202
1203	end % }}}
1204	end
1205	end

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