Context Navigation

source: issm/trunk-jpl/src/m/classes/model.m@ 16369

Last change on this file since 16369 was 16369, checked in by Eric.Larour, 11 years ago
CHG: reverting
File size: 58.9 KB

Line
1	%MODEL class definition
2	%
3	% Usage:
4	% md = model(varargin)
5
6	classdef model
7	properties (SetAccess=public) %Model fields
8	% {{{
9	%Careful here: no other class should be used as default value this is a bug of matlab
10	mesh = 0;
11	mask = 0;
12
13	geometry = 0;
14	constants = 0;
15	surfaceforcings = 0;
16	basalforcings = 0;
17	materials = 0;
18	damage = 0;
19	friction = 0;
20	flowequation = 0;
21	timestepping = 0;
22	initialization = 0;
23	rifts = 0;
24
25	debug = 0;
26	verbose = 0;
27	settings = 0;
28	toolkits = 0;
29	cluster = 0;
30
31	balancethickness = 0;
32	stressbalance = 0;
33	groundingline = 0;
34	hydrology = 0;
35	masstransport = 0;
36	thermal = 0;
37	steadystate = 0;
38	transient = 0;
39	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	%2013 October 9
96	if ~isa(md.damage,'damage'),
97	md.damage=damage();
98	md.damage.D=zeros(md.mesh.numberofvertices,1);
99	md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
100	end
101	end% }}}
102	end
103	methods
104	function md = model(varargin) % {{{
105
106	switch nargin
107	case 0
108	md=setdefaultparameters(md);
109	otherwise
110	error('model constructor error message: 0 of 1 argument only in input.');
111	end
112	end
113	%}}}
114	function md = checkmessage(md,string) % {{{
115	if(nargout~=1) error('wrong usage, model must be an output'); end
116	disp(['model not consistent: ' string]);
117	md.private.isconsistent=false;
118	end
119	%}}}
120	function md = collapse(md)% {{{
121	%COLLAPSE - collapses a 3d mesh into a 2d mesh
122	%
123	% This routine collapses a 3d model into a 2d model
124	% and collapses all the fileds of the 3d model by
125	% taking their depth-averaged values
126	%
127	% Usage:
128	% md=collapse(md)
129	%
130	% See also: EXTRUDE, MODELEXTRACT
131
132	%Check that the model is really a 3d model
133	if ~md.mesh.dimension==3,
134	error('collapse error message: only 3d mesh can be collapsed')
135	end
136
137	%Start with changing alle the fields from the 3d mesh
138
139	%drag is limited to nodes that are on the bedrock.
140	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
141
142	%p and q (same deal, except for element that are on the bedrock: )
143	md.friction.p=project2d(md,md.friction.p,1);
144	md.friction.q=project2d(md,md.friction.q,1);
145
146	%observations
147	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
148	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
149	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
150	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
151	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
152	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
153	if ~isnan(md.surfaceforcings.mass_balance),
154	md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers);
155	end;
156	if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
157
158	%results
159	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
160	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
161	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
162	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
163	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
164
165	%gia
166	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
167	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
168
169	%bedinfo and surface info
170	md.mesh.elementonbed=ones(md.mesh.numberofelements2d,1);
171	md.mesh.elementonsurface=ones(md.mesh.numberofelements2d,1);
172	md.mesh.vertexonbed=ones(md.mesh.numberofvertices2d,1);
173	md.mesh.vertexonsurface=ones(md.mesh.numberofvertices2d,1);
174
175	%elementstype
176	if ~isnan(md.flowequation.element_equation)
177	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
178	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
179	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
180	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
181	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
182	end
183
184	%boundary conditions
185	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
186	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
187	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
188	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
189	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
190	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
191	md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers)
192	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
193
194	%materials
195	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
196	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
197
198	%damage:
199	md.damage.D=DepthAverage(md,md.damage.D);
200
201	%special for thermal modeling:
202	md.basalforcings.melting_rate=project2d(md,md.basalforcings.melting_rate,1);
203	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
204
205	%update of connectivity matrix
206	md.mesh.average_vertex_connectivity=25;
207
208	%Collapse the mesh
209	nodes2d=md.mesh.numberofvertices2d;
210	elements2d=md.mesh.numberofelements2d;
211
212	%parameters
213	md.geometry.surface=project2d(md,md.geometry.surface,1);
214	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
215	md.geometry.bed=project2d(md,md.geometry.bed,1);
216	md.geometry.bathymetry=project2d(md,md.geometry.bathymetry,1);
217	md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
218	md.mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
219	md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
220	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
221
222	%lat long
223	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
224	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
225
226	%Initialize with the 2d mesh
227	md.mesh.x=md.mesh.x2d;
228	md.mesh.y=md.mesh.y2d;
229	md.mesh.z=zeros(size(md.mesh.x2d));
230	md.mesh.numberofvertices=md.mesh.numberofvertices2d;
231	md.mesh.numberofelements=md.mesh.numberofelements2d;
232	md.mesh.elements=md.mesh.elements2d;
233
234	%Keep a trace of lower and upper nodes
235	md.mesh.lowervertex=NaN;
236	md.mesh.uppervertex=NaN;
237	md.mesh.lowerelements=NaN;
238	md.mesh.upperelements=NaN;
239
240	%Remove old mesh
241	md.mesh.x2d=NaN;
242	md.mesh.y2d=NaN;
243	md.mesh.elements2d=NaN;
244	md.mesh.numberofelements2d=md.mesh.numberofelements;
245	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
246	md.mesh.numberoflayers=0;
247
248	%Update mesh type
249	md.mesh.dimension=2;
250	end % }}}
251	function md2 = extract(md,area) % {{{
252	%extract - extract a model according to an Argus contour or flag list
253	%
254	% This routine extracts a submodel from a bigger model with respect to a given contour
255	% md must be followed by the corresponding exp file or flags list
256	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
257	% If user wants every element outside the domain to be
258	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
259	% an empty string '' will be considered as an empty domain
260	% a string 'all' will be considered as the entire domain
261	%
262	% Usage:
263	% md2=extract(md,area);
264	%
265	% Examples:
266	% md2=extract(md,'Domain.exp');
267	%
268	% See also: EXTRUDE, COLLAPSE
269
270	%copy model
271	md1=md;
272
273	%some checks
274	if ((nargin~=2) \| (nargout~=1)),
275	help extract
276	error('extract error message: bad usage');
277	end
278
279	%get elements that are inside area
280	flag_elem=FlagElements(md1,area);
281	if ~any(flag_elem),
282	error('extracted model is empty');
283	end
284
285	%kick out all elements with 3 dirichlets
286	spc_elem=find(~flag_elem);
287	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
288	flag=ones(md1.mesh.numberofvertices,1);
289	flag(spc_node)=0;
290	pos=find(sum(flag(md1.mesh.elements),2)==0);
291	flag_elem(pos)=0;
292
293	%extracted elements and nodes lists
294	pos_elem=find(flag_elem);
295	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
296
297	%keep track of some fields
298	numberofvertices1=md1.mesh.numberofvertices;
299	numberofelements1=md1.mesh.numberofelements;
300	numberofvertices2=length(pos_node);
301	numberofelements2=length(pos_elem);
302	flag_node=zeros(numberofvertices1,1);
303	flag_node(pos_node)=1;
304
305	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
306	Pelem=zeros(numberofelements1,1);
307	Pelem(pos_elem)=[1:numberofelements2]';
308	Pnode=zeros(numberofvertices1,1);
309	Pnode(pos_node)=[1:numberofvertices2]';
310
311	%renumber the elements (some nodes won't exist anymore)
312	elements_1=md1.mesh.elements;
313	elements_2=elements_1(pos_elem,:);
314	elements_2(:,1)=Pnode(elements_2(:,1));
315	elements_2(:,2)=Pnode(elements_2(:,2));
316	elements_2(:,3)=Pnode(elements_2(:,3));
317	if md1.mesh.dimension==3,
318	elements_2(:,4)=Pnode(elements_2(:,4));
319	elements_2(:,5)=Pnode(elements_2(:,5));
320	elements_2(:,6)=Pnode(elements_2(:,6));
321	end
322
323	%OK, now create the new model!
324
325	%take every field from model
326	md2=md1;
327
328	%automatically modify fields
329
330	%loop over model fields
331	model_fields=fields(md1);
332	for i=1:length(model_fields),
333	%get field
334	field=md1.(model_fields{i});
335	fieldsize=size(field);
336	if isobject(field), %recursive call
337	object_fields=fields(md1.(model_fields{i}));
338	for j=1:length(object_fields),
339	%get field
340	field=md1.(model_fields{i}).(object_fields{j});
341	fieldsize=size(field);
342	%size = number of nodes * n
343	if fieldsize(1)==numberofvertices1
344	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
345	elseif (fieldsize(1)==numberofvertices1+1)
346	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
347	%size = number of elements * n
348	elseif fieldsize(1)==numberofelements1
349	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
350	end
351	end
352	else
353	%size = number of nodes * n
354	if fieldsize(1)==numberofvertices1
355	md2.(model_fields{i})=field(pos_node,:);
356	elseif (fieldsize(1)==numberofvertices1+1)
357	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
358	%size = number of elements * n
359	elseif fieldsize(1)==numberofelements1
360	md2.(model_fields{i})=field(pos_elem,:);
361	end
362	end
363	end
364
365	%modify some specific fields
366
367	%Mesh
368	md2.mesh.numberofelements=numberofelements2;
369	md2.mesh.numberofvertices=numberofvertices2;
370	md2.mesh.elements=elements_2;
371
372	%mesh.uppervertex mesh.lowervertex
373	if md1.mesh.dimension==3
374	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
375	pos=find(~isnan(md2.mesh.uppervertex));
376	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
377
378	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
379	pos=find(~isnan(md2.mesh.lowervertex));
380	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
381
382	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
383	pos=find(~isnan(md2.mesh.upperelements));
384	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
385
386	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
387	pos=find(~isnan(md2.mesh.lowerelements));
388	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
389	end
390
391	%Initial 2d mesh
392	if md1.mesh.dimension==3
393	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
394	pos_elem_2d=find(flag_elem_2d);
395	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
396	pos_node_2d=find(flag_node_2d);
397
398	md2.mesh.numberofelements2d=length(pos_elem_2d);
399	md2.mesh.numberofvertices2d=length(pos_node_2d);
400	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
401	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
402	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
403	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
404
405	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
406	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
407	end
408
409	%Edges
410	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
411	%renumber first two columns
412	pos=find(md2.mesh.edges(:,4)~=-1);
413	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
414	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
415	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
416	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
417	%remove edges when the 2 vertices are not in the domain.
418	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
419	%Replace all zeros by -1 in the last two columns
420	pos=find(md2.mesh.edges(:,3)==0);
421	md2.mesh.edges(pos,3)=-1;
422	pos=find(md2.mesh.edges(:,4)==0);
423	md2.mesh.edges(pos,4)=-1;
424	%Invert -1 on the third column with last column (Also invert first two columns!!)
425	pos=find(md2.mesh.edges(:,3)==-1);
426	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
427	md2.mesh.edges(pos,4)=-1;
428	values=md2.mesh.edges(pos,2);
429	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
430	md2.mesh.edges(pos,1)=values;
431	%Finally remove edges that do not belong to any element
432	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
433	md2.mesh.edges(pos,:)=[];
434	end
435
436	%Penalties
437	if ~isnan(md2.stressbalance.vertex_pairing),
438	for i=1:size(md1.stressbalance.vertex_pairing,1);
439	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
440	end
441	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
442	end
443	if ~isnan(md2.masstransport.vertex_pairing),
444	for i=1:size(md1.masstransport.vertex_pairing,1);
445	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
446	end
447	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
448	end
449
450	%recreate segments
451	if md1.mesh.dimension==2
452	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
453	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
454	md2.mesh.segments=contourenvelope(md2);
455	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
456	else
457	%First do the connectivity for the contourenvelope in 2d
458	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
459	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
460	md2.mesh.segments=contourenvelope(md2);
461	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
462	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
463	%Then do it for 3d as usual
464	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
465	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
466	end
467
468	%Boundary conditions: Dirichlets on new boundary
469	%Catch the elements that have not been extracted
470	orphans_elem=find(~flag_elem);
471	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
472	%Figure out which node are on the boundary between md2 and md1
473	nodestoflag1=intersect(orphans_node,pos_node);
474	nodestoflag2=Pnode(nodestoflag1);
475	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
476	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
477	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
478	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
479	else
480	md2.stressbalance.spcvx(nodestoflag2)=NaN;
481	md2.stressbalance.spcvy(nodestoflag2)=NaN;
482	disp(' ')
483	disp('!! extract warning: spc values should be checked !!')
484	disp(' ')
485	end
486	%put 0 for vz
487	md2.stressbalance.spcvz(nodestoflag2)=0;
488	end
489	if ~isnan(md1.thermal.spctemperature),
490	md2.thermal.spctemperature(nodestoflag2,1)=1;
491	end
492
493	%Results fields
494	if isstruct(md1.results),
495	md2.results=struct();
496	solutionfields=fields(md1.results);
497	for i=1:length(solutionfields),
498	if isstruct(md1.results.(solutionfields{i}))
499	%get subfields
500	solutionsubfields=fields(md1.results.(solutionfields{i}));
501	for j=1:length(solutionsubfields),
502	field=md1.results.(solutionfields{i}).(solutionsubfields{j});
503	if length(field)==numberofvertices1,
504	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
505	elseif length(field)==numberofelements1,
506	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
507	else
508	md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
509	end
510	end
511	else
512	field=md1.results.(solutionfields{i});
513	if length(field)==numberofvertices1,
514	md2.results.(solutionfields{i})=field(pos_node);
515	elseif length(field)==numberofelements1,
516	md2.results.(solutionfields{i})=field(pos_elem);
517	else
518	md2.results.(solutionfields{i})=field;
519	end
520	end
521	end
522	end
523
524	%Keep track of pos_node and pos_elem
525	md2.mesh.extractedvertices=pos_node;
526	md2.mesh.extractedelements=pos_elem;
527	end % }}}
528	function md = extrude(md,varargin) % {{{
529	%EXTRUDE - vertically extrude a 2d mesh
530	%
531	% vertically extrude a 2d mesh and create corresponding 3d mesh.
532	% The vertical distribution can:
533	% - follow a polynomial law
534	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
535	% - be discribed by a list of coefficients (between 0 and 1)
536	%
537	%
538	% Usage:
539	% md=extrude(md,numlayers,extrusionexponent);
540	% md=extrude(md,numlayers,lowerexponent,upperexponent);
541	% md=extrude(md,listofcoefficients);
542	%
543	% Example:
544	% md=extrude(md,8,3);
545	% md=extrude(md,8,3,2);
546	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
547	%
548	% See also: MODELEXTRACT, COLLAPSE
549
550	%some checks on list of arguments
551	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
552	help extrude;
553	error('extrude error message');
554	end
555
556	%Extrude the mesh
557	if nargin==2, %list of coefficients
558	clist=varargin{1};
559	if any(clist<0) \| any(clist>1),
560	error('extrusioncoefficients must be between 0 and 1');
561	end
562	extrusionlist=sort(unique([clist(:);0;1]));
563	numlayers=length(extrusionlist);
564	elseif nargin==3, %one polynomial law
565	if varargin{2}<=0,
566	help extrude;
567	error('extrusionexponent must be >=0');
568	end
569	numlayers=varargin{1};
570	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
571	elseif nargin==4, %two polynomial laws
572	numlayers=varargin{1};
573	lowerexp=varargin{2};
574	upperexp=varargin{3};
575
576	if varargin{2}<=0 \| varargin{3}<=0,
577	help extrude;
578	error('lower and upper extrusionexponents must be >=0');
579	end
580
581	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
582	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
583	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
584
585	end
586
587	if numlayers<2,
588	error('number of layers should be at least 2');
589	end
590	if md.mesh.dimension==3,
591	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
592	end
593
594	%Initialize with the 2d mesh
595	x3d=[];
596	y3d=[];
597	z3d=[]; %the lower node is on the bed
598	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
599	bed3d=md.geometry.bed;
600
601	%Create the new layers
602	for i=1:numlayers,
603	x3d=[x3d; md.mesh.x];
604	y3d=[y3d; md.mesh.y];
605	%nodes are distributed between bed and surface accordingly to the given exponent
606	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
607	end
608	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
609
610	%Extrude elements
611	elements3d=[];
612	for i=1:numlayers-1,
613	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
614	end
615	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
616
617	%Keep a trace of lower and upper nodes
618	mesh.lowervertex=NaN*ones(number_nodes3d,1);
619	mesh.uppervertex=NaN*ones(number_nodes3d,1);
620	mesh.lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
621	mesh.uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
622	md.mesh.lowervertex=mesh.lowervertex;
623	md.mesh.uppervertex=mesh.uppervertex;
624
625	%same for lower and upper elements
626	mesh.lowerelements=NaN*ones(number_el3d,1);
627	mesh.upperelements=NaN*ones(number_el3d,1);
628	mesh.lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
629	mesh.upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
630	md.mesh.lowerelements=mesh.lowerelements;
631	md.mesh.upperelements=mesh.upperelements;
632
633	%Save old mesh
634	md.mesh.x2d=md.mesh.x;
635	md.mesh.y2d=md.mesh.y;
636	md.mesh.elements2d=md.mesh.elements;
637	md.mesh.numberofelements2d=md.mesh.numberofelements;
638	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
639
640	%Update mesh type
641	md.mesh.dimension=3;
642
643	%Build global 3d mesh
644	md.mesh.elements=elements3d;
645	md.mesh.x=x3d;
646	md.mesh.y=y3d;
647	md.mesh.z=z3d;
648	md.mesh.numberofelements=number_el3d;
649	md.mesh.numberofvertices=number_nodes3d;
650	md.mesh.numberoflayers=numlayers;
651
652	%Ok, now deal with the other fields from the 2d mesh:
653
654	%lat long
655	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
656	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
657
658	%drag coefficient is limited to nodes that are on the bedrock.
659	md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1);
660
661	%p and q (same deal, except for element that are on the bedrock: )
662	md.friction.p=project3d(md,'vector',md.friction.p,'type','element');
663	md.friction.q=project3d(md,'vector',md.friction.q,'type','element');
664
665	%observations
666	md.inversion.vx_obs=project3d(md,'vector',md.inversion.vx_obs,'type','node');
667	md.inversion.vy_obs=project3d(md,'vector',md.inversion.vy_obs,'type','node');
668	md.inversion.vel_obs=project3d(md,'vector',md.inversion.vel_obs,'type','node');
669	md.surfaceforcings.mass_balance=project3d(md,'vector',md.surfaceforcings.mass_balance,'type','node');
670	md.surfaceforcings.precipitation=project3d(md,'vector',md.surfaceforcings.precipitation,'type','node');
671	md.balancethickness.thickening_rate=project3d(md,'vector',md.balancethickness.thickening_rate,'type','node');
672	md.surfaceforcings.monthlytemperatures=project3d(md,'vector',md.surfaceforcings.monthlytemperatures,'type','node');
673
674	%results
675	if ~isnan(md.initialization.vx),md.initialization.vx=project3d(md,'vector',md.initialization.vx,'type','node');end;
676	if ~isnan(md.initialization.vy),md.initialization.vy=project3d(md,'vector',md.initialization.vy,'type','node');end;
677	if ~isnan(md.initialization.vz),md.initialization.vz=project3d(md,'vector',md.initialization.vz,'type','node');end;
678	if ~isnan(md.initialization.vel),md.initialization.vel=project3d(md,'vector',md.initialization.vel,'type','node');end;
679	if ~isnan(md.initialization.temperature),md.initialization.temperature=project3d(md,'vector',md.initialization.temperature,'type','node');end;
680	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project3d(md,'vector',md.initialization.waterfraction,'type','node');end;
681	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project3d(md,'vector',md.initialization.watercolumn,'type','node','layer',1);end;
682
683	%bedinfo and surface info
684	md.mesh.elementonbed=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',1);
685	md.mesh.elementonsurface=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',md.mesh.numberoflayers-1);
686	md.mesh.vertexonbed=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
687	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
688
689	%elementstype
690	if ~isnan(md.flowequation.element_equation)
691	oldelements_type=md.flowequation.element_equation;
692	md.flowequation.element_equation=zeros(number_el3d,1);
693	md.flowequation.element_equation=project3d(md,'vector',oldelements_type,'type','element');
694	end
695
696	%verticestype
697	if ~isnan(md.flowequation.vertex_equation)
698	oldvertices_type=md.flowequation.vertex_equation;
699	md.flowequation.vertex_equation=zeros(number_nodes3d,1);
700	md.flowequation.vertex_equation=project3d(md,'vector',oldvertices_type,'type','node');
701	end
702	md.flowequation.borderSSA=project3d(md,'vector',md.flowequation.borderSSA,'type','node');
703	md.flowequation.borderHO=project3d(md,'vector',md.flowequation.borderHO,'type','node');
704	md.flowequation.borderFS=project3d(md,'vector',md.flowequation.borderFS,'type','node');
705
706	%boundary conditions
707	md.stressbalance.spcvx=project3d(md,'vector',md.stressbalance.spcvx,'type','node');
708	md.stressbalance.spcvy=project3d(md,'vector',md.stressbalance.spcvy,'type','node');
709	md.stressbalance.spcvz=project3d(md,'vector',md.stressbalance.spcvz,'type','node');
710	md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',NaN);
711	md.masstransport.spcthickness=project3d(md,'vector',md.masstransport.spcthickness,'type','node');
712	md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
713	md.damage.spcdamage=project3d(md,'vector',md.damage.spcdamage,'type','node');
714	md.stressbalance.referential=project3d(md,'vector',md.stressbalance.referential,'type','node');
715	md.stressbalance.loadingforce=project3d(md,'vector',md.stressbalance.loadingforce,'type','node');
716
717	%connectivity
718	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
719	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
720	for i=2:numlayers-1,
721	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
722	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
723	end
724	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
725
726	%materials
727	md.materials.rheology_B=project3d(md,'vector',md.materials.rheology_B,'type','node');
728	md.materials.rheology_n=project3d(md,'vector',md.materials.rheology_n,'type','element');
729
730	%damage
731	md.damage.D=project3d(md,'vector',md.damage.D,'type','node');
732
733	%parameters
734	md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
735	md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
736	md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node');
737	md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node');
738	md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
739	md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
740	md.geometry.bathymetry=project3d(md,'vector',md.geometry.bathymetry,'type','node');
741	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
742	md.mask.groundedice_levelset=project3d(md,'vector',md.mask.groundedice_levelset,'type','node');
743	md.mask.ice_levelset=project3d(md,'vector',md.mask.ice_levelset,'type','node');
744	if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end;
745	if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end;
746	if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end;
747	if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end
748	if(md.surfaceforcings.isdelta18o),md.surfaceforcings.temperatures_lgm=project3d(md,'vector',md.surfaceforcings.temperatures_lgm,'type','node');end
749	if(md.surfaceforcings.isdelta18o),md.surfaceforcings.temperatures_presentday=project3d(md,'vector',md.surfaceforcings.temperatures_presentday,'type','node');end
750	if(md.surfaceforcings.isdelta18o),md.surfaceforcings.precipitations_presentday=project3d(md,'vector',md.surfaceforcings.precipitations_presentday,'type','node');end
751
752	%Put lithostatic pressure if there is an existing pressure
753	if ~isnan(md.initialization.pressure),
754	md.initialization.pressure=md.constants.gmd.materials.rho_ice(md.geometry.surface-md.mesh.z);
755	end
756
757	%special for thermal modeling:
758	md.basalforcings.melting_rate=project3d(md,'vector',md.basalforcings.melting_rate,'type','node','layer',1);
759	if ~isnan(md.basalforcings.geothermalflux)
760	md.basalforcings.geothermalflux=project3d(md,'vector',md.basalforcings.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux
761	end
762
763	%increase connectivity if less than 25:
764	if md.mesh.average_vertex_connectivity<=25,
765	md.mesh.average_vertex_connectivity=100;
766	end
767	end % }}}
768	function md = structtomodel(md,structmd) % {{{
769
770	if ~isstruct(structmd) error('input model is not a structure'); end
771
772	%loaded model is a struct, initialize output and recover all fields
773	md = structtoobj(model,structmd);
774
775	%Old field now classes
776	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
777	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
778
779	%Field name change
780	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
781	if isfield(structmd,'p'), md.friction.p=structmd.p; end
782	if isfield(structmd,'q'), md.friction.q=structmd.p; end
783	if isfield(structmd,'melting'), md.basalforcings.melting_rate=structmd.melting; end
784	if isfield(structmd,'melting_rate'), md.basalforcings.melting_rate=structmd.melting_rate; end
785	if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
786	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
787	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
788	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
789	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
790	if isfield(structmd,'gridonbed'), md.mesh.vertexonbed=structmd.gridonbed; end
791	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
792	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
793	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
794	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
795	if isfield(structmd,'g'), md.constants.g=structmd.g; end
796	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
797	if isfield(structmd,'surface_mass_balance'), md.surfaceforcings.mass_balance=structmd.surface_mass_balance; end
798	if isfield(structmd,'basal_melting_rate'), md.basalforcings.melting_rate=structmd.basal_melting_rate; end
799	if isfield(structmd,'basal_melting_rate_correction'), md.basalforcings.melting_rate_correction=structmd.basal_melting_rate_correction; end
800	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
801	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
802	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
803	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
804	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
805	if isfield(structmd,'riftproperties'), %old implementation
806	md.rifts=rifts();
807	md.rifts.riftproperties=structmd.riftproperties;
808	md.rifts.riftstruct=structmd.rifts;
809	md.rifts.riftproperties=structmd.riftinfo;
810	end
811	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
812	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
813	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
814	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
815	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
816	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
817	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
818	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
819	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
820	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
821	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
822	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
823	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
824	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
825	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
826	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
827	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
828	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
829	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
830	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
831	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
832	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
833	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
834	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
835	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
836	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
837	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
838	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
839	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
840	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
841	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
842	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
843	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
844	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
845	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
846	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
847	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
848	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
849	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
850	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
851	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
852	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
853	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
854	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
855	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
856	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
857	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
858	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
859	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
860	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
861	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
862	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
863	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
864	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
865	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
866	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
867	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
868	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
869	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
870	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
871	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
872	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
873	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
874	if isfield(structmd,'bed'), md.geometry.bed=structmd.bed; end
875	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
876	if isfield(structmd,'bathymetry'), md.geometry.bathymetry=structmd.bathymetry; end
877	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
878	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
879	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
880	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
881	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
882	if isfield(structmd,'hemisphere'), md.mesh.hemisphere=structmd.hemisphere; end
883	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
884	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
885	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
886	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
887	if isfield(structmd,'dim'), md.mesh.dimension=structmd.dim; end
888	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
889	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
890	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
891	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
892	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
893	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
894	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
895	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
896	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
897	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
898	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
899	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
900	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
901	if isfield(structmd,'elementonbed'), md.mesh.elementonbed=structmd.elementonbed; end
902	if isfield(structmd,'elementonsurface'), md.mesh.elementonsurface=structmd.elementonsurface; end
903	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
904	if isfield(structmd,'nodeonbed'), md.mesh.vertexonbed=structmd.nodeonbed; end
905	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
906	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
907	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
908	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
909	if isfield(structmd,'edges'),
910	md.mesh.edges=structmd.edges;
911	md.mesh.edges(isnan(md.mesh.edges))=-1;
912	end
913	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
914	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
915	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
916	if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
917	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
918	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
919	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
920
921	%Field changes
922	if (isfield(structmd,'type') & ischar(structmd.type)),
923	if strcmpi(structmd.type,'2d'), md.mesh.dimension=2; end
924	if strcmpi(structmd.type,'3d'), md.mesh.dimension=3; end
925	end
926	if isnumeric(md.verbose),
927	md.verbose=verbose;
928	end
929
930	if isfield(structmd,'spcvelocity'),
931	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
932	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
933	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
934	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
935	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
936	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
937	end
938	if isfield(structmd,'spcvx'),
939	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
940	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
941	end
942	if isfield(structmd,'spcvy'),
943	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
944	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
945	end
946	if isfield(structmd,'spcvz'),
947	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
948	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
949	end
950	if isfield(structmd,'pressureload'),
951	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
952	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
953	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
954	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
955	end
956	end
957	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
958	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
959	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
960	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
961	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
962	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
963	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
964	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
965	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
966	end
967	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
968	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
969	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
970	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
971	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
972	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
973	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
974	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
975	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
976	end
977	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
978	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
979	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
980	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
981	end
982	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
983	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
984	if (structmd.groundingline_migration==273), md.groundingline.migration='AgressiveMigration'; end
985	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
986	end
987	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
988	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
989	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
990	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
991	end
992	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
993	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
994	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
995	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
996	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
997	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
998	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
999	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1000	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1001	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1002	end
1003
1004	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1005	md.thermal.stabilization=2;
1006	md.masstransport.stabilization=1;
1007	md.balancethickness.stabilization=1;
1008	end
1009	if isnumeric(md.masstransport.hydrostatic_adjustment)
1010	if md.masstransport.hydrostatic_adjustment==269,
1011	md.masstransport.hydrostatic_adjustment='Incremental';
1012	else
1013	md.masstransport.hydrostatic_adjustment='Absolute';
1014	end
1015	end
1016
1017	%New fields
1018	if ~isfield(structmd,'upperelements');
1019	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1020	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1021	end
1022	if ~isfield(structmd,'lowerelements');
1023	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1024	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1025	end
1026	if ~isfield(structmd,'diagnostic_ref');
1027	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1028	end
1029	if ~isfield(structmd,'loadingforce');
1030	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1031	end
1032
1033	%2013 August 9
1034	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1035	disp('Recovering old prognostic class');
1036	md.masstransport=masstransport(structmd.prognostic);
1037	end
1038	%2013 August 9
1039	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
1040	disp('Recovering old diagnostic class');
1041	md.stressbalance=stressbalance(structmd.diagnostic);
1042	end
1043	end% }}}
1044	function md = setdefaultparameters(md) % {{{
1045
1046	%initialize subclasses
1047	md.mesh = mesh();
1048	md.mask = mask();
1049	md.constants = constants();
1050	md.geometry = geometry();
1051	md.initialization = initialization();
1052	md.surfaceforcings = surfaceforcings();
1053	md.basalforcings = basalforcings();
1054	md.friction = friction();
1055	md.rifts = rifts();
1056	md.timestepping = timestepping();
1057	md.groundingline = groundingline();
1058	md.materials = matice();
1059	md.damage = damage();
1060	md.flowequation = flowequation();
1061	md.debug = debug();
1062	md.verbose = verbose();
1063	md.settings = settings();
1064	md.toolkits = toolkits();
1065	md.cluster = generic();
1066	md.balancethickness = balancethickness();
1067	md.stressbalance = stressbalance();
1068	md.hydrology = hydrologyshreve();
1069	md.masstransport = masstransport();
1070	md.thermal = thermal();
1071	md.steadystate = steadystate();
1072	md.transient = transient();
1073	md.gia = gia();
1074	md.autodiff = autodiff();
1075	md.flaim = flaim();
1076	md.inversion = inversion();
1077	md.qmu = qmu();
1078	md.radaroverlay = radaroverlay();
1079	md.results = struct();
1080	md.miscellaneous = miscellaneous();
1081	md.private = private();
1082	end
1083	%}}}
1084	function disp(obj) % {{{
1085	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(obj.mesh) ']'],'mesh properties'));
1086	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(obj.mask) ']'],'defines grounded and floating elements'));
1087	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(obj.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1088	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(obj.constants) ']'],'physical constants'));
1089	disp(sprintf('%19s: %-22s -- %s','surfaceforcings' ,['[1x1 ' class(obj.surfaceforcings) ']'],'surface forcings'));
1090	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(obj.basalforcings) ']'],'bed forcings'));
1091	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(obj.materials) ']'],'material properties'));
1092	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(obj.damage) ']'],'damage propagation laws'));
1093	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(obj.friction) ']'],'basal friction/drag properties'));
1094	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(obj.flowequation) ']'],'flow equations'));
1095	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(obj.timestepping) ']'],'time stepping for transient models'));
1096	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(obj.initialization) ']'],'initial guess/state'));
1097	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(obj.rifts) ']'],'rifts properties'));
1098	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(obj.debug) ']'],'debugging tools (valgrind, gprof)'));
1099	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
1100	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
1101	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(obj.toolkits) ']'],'PETSc options for each solution'));
1102	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
1103	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
1104	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(obj.stressbalance) ']'],'parameters for stressbalance solution'));
1105	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(obj.groundingline) ']'],'parameters for groundingline solution'));
1106	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(obj.hydrology) ']'],'parameters for hydrology solution'));
1107	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(obj.masstransport) ']'],'parameters for masstransport solution'));
1108	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(obj.thermal) ']'],'parameters for thermal solution'));
1109	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
1110	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
1111	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(obj.gia) ']'],'parameters for gia solution'));
1112	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
1113	disp(sprintf('%19s: %-22s -- %s','flaim' ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
1114	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(obj.inversion) ']'],'parameters for inverse methods'));
1115	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(obj.qmu) ']'],'dakota properties'));
1116	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(obj.results) ']'],'model results'));
1117	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(obj.radaroverlay) ']'],'radar image for plot overlay'));
1118	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields'));
1119	end % }}}
1120	function memory(obj) % {{{
1121
1122	disp(sprintf('\nMemory imprint:\n'));
1123
1124	fields=properties('model');
1125	mem=0;
1126
1127	for i=1:length(fields),
1128	field=obj.(fields{i});
1129	s=whos('field');
1130	mem=mem+s.bytes/1e6;
1131	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1132	end
1133	disp(sprintf('%19s--%10s','--------------','--------------'));
1134	disp(sprintf('%19s: %g Mb','Total',mem));
1135	end % }}}
1136	function netcdf(obj,filename) % {{{
1137	%NETCDF - save model as netcdf
1138	%
1139	% Usage:
1140	% netcdf(md,filename)
1141	%
1142	% Example:
1143	% netcdf(md,'model.nc');
1144
1145	disp('Saving model as NetCDF');
1146	%1. Create NetCDF file
1147	ncid=netcdf.create(filename,'CLOBBER');
1148	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1149	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' obj.miscellaneous.name ')']);
1150	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1151	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1152
1153	%Preallocate variable id, needed to write variables in netcdf file
1154	var_id=zeros(1000,1);%preallocate
1155
1156	for step=1:2,
1157	counter=0;
1158	[var_id,counter]=structtonc(ncid,'md',obj,0,var_id,counter,step);
1159	if step==1, netcdf.endDef(ncid); end
1160	end
1161
1162	if counter>1000,
1163	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1164	end
1165
1166	netcdf.close(ncid)
1167	end % }}}
1168	function xylim(obj) % {{{
1169
1170	xlim([min(obj.mesh.x) max(obj.mesh.x)]);
1171	ylim([min(obj.mesh.y) max(obj.mesh.y)])
1172	end % }}}
1173	function md=upload(md) % {{{
1174	%the goal of this routine is to upload the model onto a server, and to empty it.
1175	%So first, save the model with a unique name and upload the file to the server:
1176	random_part=fix(rand(1)*10000);
1177	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1178	eval(['save ' id ' md']);
1179
1180	%Now, upload the file:
1181	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1182
1183	%Now, empty this model of everything except settings, and record name of file we just uploaded!
1184	settings_back=md.settings;
1185	md=model();
1186	md.settings=settings_back;
1187	md.settings.upload_filename=id;
1188
1189	%get locally rid of file that was uploaded
1190	eval(['delete ' id]);
1191
1192	end % }}}
1193	function md=download(md) % {{{
1194
1195	%the goal of this routine is to download the internals of the current model from a server, because
1196	%this model is empty, except for the settings which tell us where to go and find this model!
1197
1198	%Download the file:
1199	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1200
1201	name=md.settings.upload_filename;
1202
1203	%Now, load this model:
1204	md=loadmodel(md.settings.upload_filename);
1205
1206	%get locally rid of file that was downloaded
1207	eval(['delete ' name]);
1208
1209	end % }}}
1210	end
1211	end

Note: See TracBrowser for help on using the repository browser.

Download in other formats: