Context Navigation

source: issm/trunk-jpl/src/m/classes/model.m@ 21428

Last change on this file since 21428 was 21428, checked in by langchar, 8 years ago
CHG: in extract, added elseif elements+1 for GEMB inputs
File size: 64.8 KB

Line
1	%MODEL class definition
2	%
3	% Usage:
4	% md = model(varargin)
5
6	classdef model
7	properties (SetAccess=public) %Model fields
8	% {{{
9	%Careful here: no other class should be used as default value this is a bug of matlab
10	mesh = 0;
11	mask = 0;
12
13	geometry = 0;
14	constants = 0;
15	smb = 0;
16	basalforcings = 0;
17	materials = 0;
18	damage = 0;
19	friction = 0;
20	flowequation = 0;
21	timestepping = 0;
22	initialization = 0;
23	rifts = 0;
24	slr = 0;
25
26	debug = 0;
27	verbose = 0;
28	settings = 0;
29	toolkits = 0;
30	cluster = 0;
31
32	balancethickness = 0;
33	stressbalance = 0;
34	groundingline = 0;
35	hydrology = 0;
36	masstransport = 0;
37	thermal = 0;
38	steadystate = 0;
39	transient = 0;
40	levelset = 0;
41	calving = 0;
42	gia = 0;
43	esa = 0;
44
45	autodiff = 0;
46	inversion = 0;
47	qmu = 0;
48
49	results = 0;
50	outputdefinition = 0;
51	radaroverlay = 0;
52	miscellaneous = 0;
53	private = 0;
54
55	%}}}
56	end
57	methods (Static)
58	function md = loadobj(md) % {{{
59	% This function is directly called by matlab when a model object is
60	% loaded. If the input is a struct it is an old version of model and
61	% old fields must be recovered (make sure they are in the deprecated
62	% model properties)
63
64	if verLessThan('matlab','7.9'),
65	disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
66	disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
67
68	% This is a Matlab bug: all the fields of md have their default value
69	% Example of error message:
70	% Warning: Error loading an object of class 'model':
71	% Undefined function or method 'exist' for input arguments of type 'cell'
72	%
73	% This has been fixed in MATLAB 7.9 (R2009b) and later versions
74	end
75
76	if isstruct(md)
77	disp('Recovering model object from a previous version');
78	md = structtomodel(model,md);
79	end
80
81	%2012 August 4th
82	if isa(md.materials,'materials'),
83	disp('Recovering old materials');
84	if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
85	md.materials=matice(md.materials);
86	else
87	md.materials=matdamageice(md.materials);
88	end
89	end
90	%2013 April 12
91	if numel(md.stressbalance.loadingforce==1)
92	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
93	end
94	%2013 April 17
95	if isa(md.hydrology,'hydrology'),
96	disp('Recovering old hydrology class');
97	md.hydrology=hydrologyshreve(md.materials);
98	end
99	%2013 October 9
100	if ~isa(md.damage,'damage'),
101	md.damage=damage();
102	md.damage.D=zeros(md.mesh.numberofvertices,1);
103	md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
104	end
105	%2013 November 18
106	if ~isa(md.outputdefinition,'outputdefinition'),
107	md.outputdefinition=outputdefinition();
108	end
109	%2014 March 26th
110	if isa(md.mesh,'mesh'),
111	disp('Recovering old mesh class');
112	if isprop(md.mesh,'dimension'),
113	if md.mesh.dimension==2,
114	md.mesh=mesh2d(md.mesh);
115	else
116	md.mesh=mesh3dprisms(md.mesh);
117	end
118	else
119	md.mesh=mesh2dvertical(md.mesh);
120	end
121	end
122	%2014 November 12
123	if isa(md.calving,'double');
124	md.calving=calving();
125	end
126	%2016 February 3
127	if isa(md.slr,'double');
128	md.slr=slr();
129	end
130	%2016 October 11
131	if isa(md.esa,'double');
132	md.esa=esa();
133	end
134
135	end% }}}
136	end
137	methods
138	function md = model(varargin) % {{{
139
140	switch nargin
141	case 0
142	md=setdefaultparameters(md);
143	case 1
144	error('model constructor not supported yet');
145
146	otherwise
147	error('model constructor error message: 0 of 1 argument only in input.');
148	end
149	end
150	%}}}
151	function md = checkmessage(md,string) % {{{
152	if(nargout~=1) error('wrong usage, model must be an output'); end
153	disp(['model not consistent: ' string]);
154	md.private.isconsistent=false;
155	end
156	%}}}
157	function md = collapse(md)% {{{
158	%COLLAPSE - collapses a 3d mesh into a 2d mesh
159	%
160	% This routine collapses a 3d model into a 2d model
161	% and collapses all the fileds of the 3d model by
162	% taking their depth-averaged values
163	%
164	% Usage:
165	% md=collapse(md)
166	%
167	% See also: EXTRUDE, MODELEXTRACT
168
169	%Check that the model is really a 3d model
170	if ~strcmp(md.mesh.elementtype(),'Penta'),
171	error('collapse error message: only 3d mesh can be collapsed')
172	end
173
174	%Start with changing all the fields from the 3d mesh
175
176	%dealing with the friciton law
177	%drag is limited to nodes that are on the bedrock.
178	if isa(md.friction,'friction'),
179	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
180	md.friction.p=project2d(md,md.friction.p,1);
181	md.friction.q=project2d(md,md.friction.q,1);
182	elseif isa(md.friction,'frictionhydro'),
183	md.friction.q=project2d(md,md.friction.q,1);
184	md.friction.C=project2d(md,md.friction.C,1);
185	md.friction.As=project2d(md,md.friction.As,1);
186	md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
187	elseif isa(md.friction,'frictionwaterlayer'),
188	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
189	md.friction.p=project2d(md,md.friction.p,1);
190	md.friction.q=project2d(md,md.friction.q,1);
191	md.friction.water_layer=project2d(md,md.friction.water_layer,1);
192	elseif isa(md.friction,'frictionweertman'),
193	md.friction.C=project2d(md,md.friction.C,1);
194	md.friction.m=project2d(md,md.friction.m,1);
195	elseif isa(md.friction,'frictionweertmantemp'),
196	md.friction.C=project2d(md,md.friction.C,1);
197	md.friction.m=project2d(md,md.friction.m,1);
198	else
199	disp('friction type not supported');
200	end
201
202	%observations
203	if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
204	if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
205	if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
206	if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
207	if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
208	if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
209	if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
210	md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
211	elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
212	md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
213	end;
214
215	%results
216	if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
217	if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
218	if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
219	if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
220	if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
221	if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
222	if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
223	if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
224	if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
225	if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
226	if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
227	%gia
228	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
229	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
230
231	%elementstype
232	if ~isnan(md.flowequation.element_equation)
233	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
234	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
235	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
236	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
237	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
238	end
239
240	%boundary conditions
241	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
242	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
243	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
244	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
245	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
246	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
247	if ~isnan(md.damage.spcdamage), md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
248	if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
249	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
250	md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers);
251
252	% Hydrologydc variables
253	if isa(md.hydrology,'hydrologydc');
254	md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
255	md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
256	md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
257	md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
258	if(md.hydrology.isefficientlayer==1)
259	md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
260	end
261	end
262
263	%materials
264	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
265	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
266
267	%damage:
268	if md.damage.isdamage,
269	md.damage.D=DepthAverage(md,md.damage.D);
270	end
271
272	%special for thermal modeling:
273	if ~isnan(md.basalforcings.groundedice_melting_rate),
274	md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
275	end
276	if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
277	md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
278	end
279	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
280
281	if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
282	md.calving.coeff=project2d(md,md.calving.coeff,1);
283	end
284	if isprop(md.calving,'meltingrate') & ~isnan(md.calving.meltingrate),
285	md.calving.meltingrate=project2d(md,md.calving.meltingrate,1);
286	end
287
288	%update of connectivity matrix
289	md.mesh.average_vertex_connectivity=25;
290
291	%Collapse the mesh
292	nodes2d=md.mesh.numberofvertices2d;
293	elements2d=md.mesh.numberofelements2d;
294
295	%parameters
296	md.geometry.surface=project2d(md,md.geometry.surface,1);
297	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
298	md.geometry.base=project2d(md,md.geometry.base,1);
299	if ~isnan(md.geometry.bed),
300	md.geometry.bed=project2d(md,md.geometry.bed,1);
301	end
302
303	if ~isnan(md.mask.groundedice_levelset),
304	md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
305	end
306	if ~isnan(md.mask.ice_levelset),
307	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
308	end
309
310	%lat long
311	if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
312	if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
313
314	%Initialize with the 2d mesh
315	mesh=mesh2d();
316	mesh.x=md.mesh.x2d;
317	mesh.y=md.mesh.y2d;
318	mesh.numberofvertices=md.mesh.numberofvertices2d;
319	mesh.numberofelements=md.mesh.numberofelements2d;
320	mesh.elements=md.mesh.elements2d;
321	if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
322	if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
323	md.mesh=mesh;
324	md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
325	md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
326	md.mesh.segments=contourenvelope(md.mesh);
327
328	end % }}}
329	function md2 = extract(md,area) % {{{
330	%extract - extract a model according to an Argus contour or flag list
331	%
332	% This routine extracts a submodel from a bigger model with respect to a given contour
333	% md must be followed by the corresponding exp file or flags list
334	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
335	% If user wants every element outside the domain to be
336	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
337	% an empty string '' will be considered as an empty domain
338	% a string 'all' will be considered as the entire domain
339	%
340	% Usage:
341	% md2=extract(md,area);
342	%
343	% Examples:
344	% md2=extract(md,'Domain.exp');
345	%
346	% See also: EXTRUDE, COLLAPSE
347
348	%copy model
349	md1=md;
350
351	%some checks
352	if ((nargin~=2) \| (nargout~=1)),
353	help extract
354	error('extract error message: bad usage');
355	end
356
357	%get elements that are inside area
358	flag_elem=FlagElements(md1,area);
359	if ~any(flag_elem),
360	error('extracted model is empty');
361	end
362
363	%kick out all elements with 3 dirichlets
364	spc_elem=find(~flag_elem);
365	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
366	flag=ones(md1.mesh.numberofvertices,1);
367	flag(spc_node)=0;
368	pos=find(sum(flag(md1.mesh.elements),2)==0);
369	flag_elem(pos)=0;
370
371	%extracted elements and nodes lists
372	pos_elem=find(flag_elem);
373	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
374
375	%keep track of some fields
376	numberofvertices1=md1.mesh.numberofvertices;
377	numberofelements1=md1.mesh.numberofelements;
378	numberofvertices2=length(pos_node);
379	numberofelements2=length(pos_elem);
380	flag_node=zeros(numberofvertices1,1);
381	flag_node(pos_node)=1;
382
383	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
384	Pelem=zeros(numberofelements1,1);
385	Pelem(pos_elem)=[1:numberofelements2]';
386	Pnode=zeros(numberofvertices1,1);
387	Pnode(pos_node)=[1:numberofvertices2]';
388
389	%renumber the elements (some nodes won't exist anymore)
390	elements_1=md1.mesh.elements;
391	elements_2=elements_1(pos_elem,:);
392	elements_2(:,1)=Pnode(elements_2(:,1));
393	elements_2(:,2)=Pnode(elements_2(:,2));
394	elements_2(:,3)=Pnode(elements_2(:,3));
395	if isa(md1.mesh,'mesh3dprisms'),
396	elements_2(:,4)=Pnode(elements_2(:,4));
397	elements_2(:,5)=Pnode(elements_2(:,5));
398	elements_2(:,6)=Pnode(elements_2(:,6));
399	end
400
401	%OK, now create the new model!
402
403	%take every field from model
404	md2=md1;
405
406	%automatically modify fields
407
408	%loop over model fields
409	model_fields=fields(md1);
410	for i=1:length(model_fields),
411	%get field
412	field=md1.(model_fields{i});
413	fieldsize=size(field);
414	if isobject(field), %recursive call
415	object_fields=fields(md1.(model_fields{i}));
416	for j=1:length(object_fields),
417	%get field
418	field=md1.(model_fields{i}).(object_fields{j});
419	fieldsize=size(field);
420	%size = number of nodes * n
421	if fieldsize(1)==numberofvertices1
422	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
423	elseif (fieldsize(1)==numberofvertices1+1)
424	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
425	%size = number of elements * n
426	elseif fieldsize(1)==numberofelements1
427	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
428	elseif (fieldsize(1)==numberofelements1+1)
429	md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
430	end
431	end
432	else
433	%size = number of nodes * n
434	if fieldsize(1)==numberofvertices1
435	md2.(model_fields{i})=field(pos_node,:);
436	elseif (fieldsize(1)==numberofvertices1+1)
437	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
438	%size = number of elements * n
439	elseif fieldsize(1)==numberofelements1
440	md2.(model_fields{i})=field(pos_elem,:);
441	elseif (fieldsize(1)==numberofelements1+1)
442	md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
443	end
444	end
445	end
446
447	%modify some specific fields
448
449	%Mesh
450	md2.mesh.numberofelements=numberofelements2;
451	md2.mesh.numberofvertices=numberofvertices2;
452	md2.mesh.elements=elements_2;
453
454	%mesh.uppervertex mesh.lowervertex
455	if isa(md1.mesh,'mesh3dprisms'),
456	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
457	pos=find(~isnan(md2.mesh.uppervertex));
458	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
459
460	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
461	pos=find(~isnan(md2.mesh.lowervertex));
462	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
463
464	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
465	pos=find(~isnan(md2.mesh.upperelements));
466	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
467
468	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
469	pos=find(~isnan(md2.mesh.lowerelements));
470	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
471	end
472
473	%Initial 2d mesh
474	if isa(md1.mesh,'mesh3dprisms'),
475	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
476	pos_elem_2d=find(flag_elem_2d);
477	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
478	pos_node_2d=find(flag_node_2d);
479
480	md2.mesh.numberofelements2d=length(pos_elem_2d);
481	md2.mesh.numberofvertices2d=length(pos_node_2d);
482	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
483	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
484	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
485	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
486
487	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
488	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
489	end
490
491	%Edges
492	if(dimension(md.mesh)==2),
493	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
494	%renumber first two columns
495	pos=find(md2.mesh.edges(:,4)~=-1);
496	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
497	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
498	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
499	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
500	%remove edges when the 2 vertices are not in the domain.
501	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
502	%Replace all zeros by -1 in the last two columns
503	pos=find(md2.mesh.edges(:,3)==0);
504	md2.mesh.edges(pos,3)=-1;
505	pos=find(md2.mesh.edges(:,4)==0);
506	md2.mesh.edges(pos,4)=-1;
507	%Invert -1 on the third column with last column (Also invert first two columns!!)
508	pos=find(md2.mesh.edges(:,3)==-1);
509	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
510	md2.mesh.edges(pos,4)=-1;
511	values=md2.mesh.edges(pos,2);
512	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
513	md2.mesh.edges(pos,1)=values;
514	%Finally remove edges that do not belong to any element
515	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
516	md2.mesh.edges(pos,:)=[];
517	end
518	end
519
520	%Penalties
521	if ~isnan(md2.stressbalance.vertex_pairing),
522	for i=1:size(md1.stressbalance.vertex_pairing,1);
523	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
524	end
525	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
526	end
527	if ~isnan(md2.masstransport.vertex_pairing),
528	for i=1:size(md1.masstransport.vertex_pairing,1);
529	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
530	end
531	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
532	end
533
534	%recreate segments
535	if isa(md1.mesh,'mesh2d') \| isa(md1.mesh','mesh3dsurface'),
536	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
537	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
538	md2.mesh.segments=contourenvelope(md2.mesh);
539	md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
540	else
541	%First do the connectivity for the contourenvelope in 2d
542	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
543	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
544	segments=contourenvelope(md2.mesh);
545	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
546	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
547	%Then do it for 3d as usual
548	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
549	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
550	end
551
552	%Boundary conditions: Dirichlets on new boundary
553	%Catch the elements that have not been extracted
554	orphans_elem=find(~flag_elem);
555	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
556	%Figure out which node are on the boundary between md2 and md1
557	nodestoflag1=intersect(orphans_node,pos_node);
558	nodestoflag2=Pnode(nodestoflag1);
559	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
560	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
561	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
562	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
563	else
564	md2.stressbalance.spcvx(nodestoflag2)=NaN;
565	md2.stressbalance.spcvy(nodestoflag2)=NaN;
566	disp(' ')
567	disp('!! extract warning: spc values should be checked !!')
568	disp(' ')
569	end
570	%put 0 for vz
571	md2.stressbalance.spcvz(nodestoflag2)=0;
572	end
573	if ~isnan(md1.thermal.spctemperature),
574	md2.thermal.spctemperature(nodestoflag2,1)=1;
575	end
576
577	%Results fields
578	if isstruct(md1.results),
579	md2.results=struct();
580	solutionfields=fields(md1.results);
581	for i=1:length(solutionfields),
582	if isstruct(md1.results.(solutionfields{i}))
583	%get subfields
584	solutionsubfields=fields(md1.results.(solutionfields{i}));
585	for j=1:length(solutionsubfields),
586	field=md1.results.(solutionfields{i}).(solutionsubfields{j});
587	if length(field)==numberofvertices1,
588	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
589	elseif length(field)==numberofelements1,
590	md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
591	else
592	md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
593	end
594	end
595	else
596	field=md1.results.(solutionfields{i});
597	if length(field)==numberofvertices1,
598	md2.results.(solutionfields{i})=field(pos_node);
599	elseif length(field)==numberofelements1,
600	md2.results.(solutionfields{i})=field(pos_elem);
601	else
602	md2.results.(solutionfields{i})=field;
603	end
604	end
605	end
606	end
607
608	%Keep track of pos_node and pos_elem
609	md2.mesh.extractedvertices=pos_node;
610	md2.mesh.extractedelements=pos_elem;
611	end % }}}
612	function md = extrude(md,varargin) % {{{
613	%EXTRUDE - vertically extrude a 2d mesh
614	%
615	% vertically extrude a 2d mesh and create corresponding 3d mesh.
616	% The vertical distribution can:
617	% - follow a polynomial law
618	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
619	% - be discribed by a list of coefficients (between 0 and 1)
620	%
621	%
622	% Usage:
623	% md=extrude(md,numlayers,extrusionexponent);
624	% md=extrude(md,numlayers,lowerexponent,upperexponent);
625	% md=extrude(md,listofcoefficients);
626	%
627	% Example:
628	% md=extrude(md,15,1.3);
629	% md=extrude(md,15,1.3,1.2);
630	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
631	%
632	% See also: MODELEXTRACT, COLLAPSE
633
634	%some checks on list of arguments
635	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
636	help extrude;
637	error('extrude error message');
638	end
639
640	%Extrude the mesh
641	if nargin==2, %list of coefficients
642	clist=varargin{1};
643	if any(clist<0) \| any(clist>1),
644	error('extrusioncoefficients must be between 0 and 1');
645	end
646	extrusionlist=sort(unique([clist(:);0;1]));
647	numlayers=length(extrusionlist);
648	elseif nargin==3, %one polynomial law
649	if varargin{2}<=0,
650	help extrude;
651	error('extrusionexponent must be >=0');
652	end
653	numlayers=varargin{1};
654	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
655	elseif nargin==4, %two polynomial laws
656	numlayers=varargin{1};
657	lowerexp=varargin{2};
658	upperexp=varargin{3};
659
660	if varargin{2}<=0 \| varargin{3}<=0,
661	help extrude;
662	error('lower and upper extrusionexponents must be >=0');
663	end
664
665	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
666	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
667	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
668
669	end
670
671	if numlayers<2,
672	error('number of layers should be at least 2');
673	end
674	if strcmp(md.mesh.domaintype(),'3D')
675	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
676	end
677
678	%Initialize with the 2d mesh
679	mesh2d = md.mesh;
680	md.mesh=mesh3dprisms();
681	md.mesh.x = mesh2d.x;
682	md.mesh.y = mesh2d.y;
683	md.mesh.elements = mesh2d.elements;
684	md.mesh.numberofelements = mesh2d.numberofelements;
685	md.mesh.numberofvertices = mesh2d.numberofvertices;
686
687	md.mesh.lat = mesh2d.lat;
688	md.mesh.long = mesh2d.long;
689	md.mesh.epsg = mesh2d.epsg;
690
691	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
692	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
693	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
694	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
695
696	md.mesh.extractedvertices = mesh2d.extractedvertices;
697	md.mesh.extractedelements = mesh2d.extractedelements;
698
699	x3d=[];
700	y3d=[];
701	z3d=[]; %the lower node is on the bed
702	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
703	bed3d=md.geometry.base;
704
705	%Create the new layers
706	for i=1:numlayers,
707	x3d=[x3d; md.mesh.x];
708	y3d=[y3d; md.mesh.y];
709	%nodes are distributed between bed and surface accordingly to the given exponent
710	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
711	end
712	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
713
714	%Extrude elements
715	elements3d=[];
716	for i=1:numlayers-1,
717	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
718	end
719	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
720
721	%Keep a trace of lower and upper nodes
722	lowervertex=NaN*ones(number_nodes3d,1);
723	uppervertex=NaN*ones(number_nodes3d,1);
724	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
725	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
726	md.mesh.lowervertex=lowervertex;
727	md.mesh.uppervertex=uppervertex;
728
729	%same for lower and upper elements
730	lowerelements=NaN*ones(number_el3d,1);
731	upperelements=NaN*ones(number_el3d,1);
732	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
733	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
734	md.mesh.lowerelements=lowerelements;
735	md.mesh.upperelements=upperelements;
736
737	%Save old mesh
738	md.mesh.x2d=md.mesh.x;
739	md.mesh.y2d=md.mesh.y;
740	md.mesh.elements2d=md.mesh.elements;
741	md.mesh.numberofelements2d=md.mesh.numberofelements;
742	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
743
744	%Build global 3d mesh
745	md.mesh.elements=elements3d;
746	md.mesh.x=x3d;
747	md.mesh.y=y3d;
748	md.mesh.z=z3d;
749	md.mesh.numberofelements=number_el3d;
750	md.mesh.numberofvertices=number_nodes3d;
751	md.mesh.numberoflayers=numlayers;
752
753	%Ok, now deal with the other fields from the 2d mesh:
754
755	%bedinfo and surface info
756	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
757	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
758	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
759
760	%lat long
761	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
762	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
763
764	md.geometry=extrude(md.geometry,md);
765	md.friction = extrude(md.friction,md);
766	md.inversion = extrude(md.inversion,md);
767	md.smb = extrude(md.smb,md);
768	md.initialization = extrude(md.initialization,md);
769
770	md.flowequation=md.flowequation.extrude(md);
771	md.stressbalance=extrude(md.stressbalance,md);
772	md.thermal=md.thermal.extrude(md);
773	md.masstransport=md.masstransport.extrude(md);
774	md.levelset=extrude(md.levelset,md);
775	md.calving=extrude(md.calving,md);
776	md.hydrology = extrude(md.hydrology,md);
777
778	%connectivity
779	if ~isnan(md.mesh.elementconnectivity)
780	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
781	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
782	for i=2:numlayers-1,
783	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
784	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
785	end
786	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
787	end
788
789	md.materials=extrude(md.materials,md);
790	md.damage=extrude(md.damage,md);
791	md.mask=extrude(md.mask,md);
792	md.qmu=extrude(md.qmu,md);
793	md.basalforcings=extrude(md.basalforcings,md);
794
795	%increase connectivity if less than 25:
796	if md.mesh.average_vertex_connectivity<=25,
797	md.mesh.average_vertex_connectivity=100;
798	end
799	end % }}}
800	function md = structtomodel(md,structmd) % {{{
801
802	if ~isstruct(structmd) error('input model is not a structure'); end
803
804	%loaded model is a struct, initialize output and recover all fields
805	md = structtoobj(model,structmd);
806
807	%Old field now classes
808	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
809	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
810
811	%Field name change
812	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
813	if isfield(structmd,'p'), md.friction.p=structmd.p; end
814	if isfield(structmd,'q'), md.friction.q=structmd.p; end
815	if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
816	if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
817	if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
818	if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
819	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
820	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
821	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
822	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
823	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
824	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
825	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
826	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
827	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
828	if isfield(structmd,'g'), md.constants.g=structmd.g; end
829	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
830	if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
831	if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
832	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
833	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
834	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
835	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
836	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
837	if isfield(structmd,'riftproperties'), %old implementation
838	md.rifts=rifts();
839	md.rifts.riftproperties=structmd.riftproperties;
840	md.rifts.riftstruct=structmd.rifts;
841	md.rifts.riftproperties=structmd.riftinfo;
842	end
843	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
844	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
845	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
846	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
847	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
848	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
849	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
850	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
851	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
852	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
853	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
854	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
855	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
856	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
857	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
858	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
859	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
860	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
861	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
862	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
863	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
864	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
865	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
866	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
867	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
868	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
869	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
870	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
871	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
872	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
873	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
874	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
875	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
876	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
877	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
878	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
879	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
880	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
881	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
882	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
883	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
884	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
885	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
886	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
887	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
888	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
889	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
890	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
891	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
892	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
893	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
894	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
895	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
896	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
897	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
898	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
899	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
900	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
901	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
902	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
903	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
904	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
905	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
906	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
907	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
908	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
909	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
910	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
911	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
912	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
913	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
914	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
915	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
916	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
917	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
918	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
919	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
920	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
921	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
922	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
923	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
924	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
925	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
926	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
927	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
928	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
929	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
930	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
931	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
932	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
933	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
934	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
935	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
936	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
937	if isfield(structmd,'edges'),
938	md.mesh.edges=structmd.edges;
939	md.mesh.edges(isnan(md.mesh.edges))=-1;
940	end
941	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
942	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
943	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
944	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
945	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
946	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
947
948	if isnumeric(md.verbose),
949	md.verbose=verbose;
950	end
951
952	if isfield(structmd,'spcvelocity'),
953	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
954	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
955	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
956	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
957	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
958	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
959	end
960	if isfield(structmd,'spcvx'),
961	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
962	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
963	end
964	if isfield(structmd,'spcvy'),
965	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
966	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
967	end
968	if isfield(structmd,'spcvz'),
969	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
970	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
971	end
972	if isfield(structmd,'pressureload'),
973	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
974	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
975	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
976	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
977	end
978	end
979	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
980	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
981	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
982	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
983	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
984	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
985	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
986	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
987	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
988	end
989	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
990	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
991	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
992	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
993	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
994	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
995	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
996	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
997	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
998	end
999	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
1000	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
1001	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1002	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1003	end
1004	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1005	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1006	if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
1007	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1008	end
1009	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1010	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1011	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1012	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1013	end
1014	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1015	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1016	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1017	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1018	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1019	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1020	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1021	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1022	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1023	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1024	end
1025
1026	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1027	md.thermal.stabilization=2;
1028	md.masstransport.stabilization=1;
1029	md.balancethickness.stabilization=1;
1030	end
1031	if isnumeric(md.masstransport.hydrostatic_adjustment)
1032	if md.masstransport.hydrostatic_adjustment==269,
1033	md.masstransport.hydrostatic_adjustment='Incremental';
1034	else
1035	md.masstransport.hydrostatic_adjustment='Absolute';
1036	end
1037	end
1038
1039	%New fields
1040	if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
1041	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1042	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1043	end
1044	if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
1045	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1046	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1047	end
1048	if ~isfield(structmd,'diagnostic_ref');
1049	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1050	end
1051	if ~isfield(structmd,'loadingforce');
1052	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1053	end
1054
1055	%2013 August 9
1056	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1057	disp('Recovering old prognostic class');
1058	md.masstransport=masstransport(structmd.prognostic);
1059	end
1060	%2013 August 9
1061	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
1062	disp('Recovering old diagnostic class');
1063	md.stressbalance=stressbalance(structmd.diagnostic);
1064	end
1065	%2014 January 9th
1066	if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
1067	disp('Recovering old surfaceforcings class');
1068	mass_balance=structmd.surfaceforcings.mass_balance;
1069	md.smb=SMB();
1070	md.smb.mass_balance=mass_balance;
1071	end
1072	%2015 September 10
1073	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
1074	disp('Recovering old SMB class');
1075	md.smb=SMBforcing(structmd.surfaceforcings);
1076	end
1077	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
1078	disp('Recovering old SMBhenning class');
1079	md.smb=SMBhenning(structmd.surfaceforcings);
1080	end
1081
1082	end% }}}
1083	function md = setdefaultparameters(md) % {{{
1084
1085	%initialize subclasses
1086	md.mesh = mesh2d();
1087	md.mask = mask();
1088	md.constants = constants();
1089	md.geometry = geometry();
1090	md.initialization = initialization();
1091	md.smb = SMBforcing();
1092	md.basalforcings = basalforcings();
1093	md.friction = friction();
1094	md.rifts = rifts();
1095	md.slr = slr();
1096	md.timestepping = timestepping();
1097	md.groundingline = groundingline();
1098	md.materials = matice();
1099	md.damage = damage();
1100	md.flowequation = flowequation();
1101	md.debug = debug();
1102	md.verbose = verbose();
1103	md.settings = settings();
1104	md.toolkits = toolkits();
1105	md.cluster = generic();
1106	md.balancethickness = balancethickness();
1107	md.stressbalance = stressbalance();
1108	md.hydrology = hydrologyshreve();
1109	md.masstransport = masstransport();
1110	md.thermal = thermal();
1111	md.steadystate = steadystate();
1112	md.transient = transient();
1113	md.levelset = levelset();
1114	md.calving = calving();
1115	md.gia = gia();
1116	md.esa = esa();
1117	md.autodiff = autodiff();
1118	md.inversion = inversion();
1119	md.qmu = qmu();
1120	md.radaroverlay = radaroverlay();
1121	md.results = struct();
1122	md.outputdefinition = outputdefinition();
1123	md.miscellaneous = miscellaneous();
1124	md.private = private();
1125	end
1126	%}}}
1127	function md = tetras(md,varargin) % {{{
1128	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1129	%
1130	% Usage:
1131	% md=tetra(md)
1132
1133	if ~isa(md.mesh,'mesh3dprisms')
1134	error('mesh is not a 3d prismatic mesh');
1135	end
1136
1137	%Initialize tetra mesh
1138	md.mesh=mesh3dtetras(md.mesh);
1139
1140	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
1141	steiner = 0;
1142	nbv = md.mesh.numberofvertices;
1143	nbt = 3*md.mesh.numberofelements;
1144	elements = zeros(nbt,4);
1145	for i=1:md.mesh.numberofelements
1146	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
1147	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
1148	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1149	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1150	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1151	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1152	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1153	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1154	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
1155	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
1156	elements(end+1,:) = [v2 v3 v5 v7];
1157	elements(end+1,:) = [v3 v5 v6 v7];
1158	elements(end+1,:) = [v1 v3 v6 v7];
1159	elements(end+1,:) = [v1 v4 v6 v7];
1160	elements(end+1,:) = [v4 v5 v6 v7];
1161	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1162	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
1163	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1164	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1165	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1166	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1167	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
1168	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1169	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1170	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1171	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1172	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
1173	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1174	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1175	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1176	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
1177	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1178	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1179	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
1180	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1181	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1182	elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
1183	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1184	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1185	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1186	elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
1187	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1188	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
1189	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1190	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1191	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1192	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1193	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1194	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1195	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
1196	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
1197	elements(end+1,:) = [v2 v5 v6 v7];
1198	elements(end+1,:) = [v2 v3 v6 v7];
1199	elements(end+1,:) = [v3 v4 v6 v7];
1200	elements(end+1,:) = [v1 v3 v4 v7];
1201	elements(end+1,:) = [v4 v5 v6 v7];
1202	else
1203	error('Case not supported'); %not supposed to happen!
1204	end
1205	%Reorder elements to make sure they are direct
1206	for j=1:3
1207	element = elements(3*(i-1)+j,:);
1208	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
1209	if det(matrix)>0,
1210	elements(3*(i-1)+j,1)=element(2);
1211	elements(3*(i-1)+j,2)=element(1);
1212	end
1213	end
1214	end
1215	%%Split in 3 tetras
1216	%subelement1 = [1 2 3 5];
1217	%subelement2 = [4 6 5 1];
1218	%subelement3 = [5 6 3 1];
1219	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
1220	if steiner==0,
1221	disp('No Steiner point required to split prismatic mesh into tets');
1222	else
1223	disp([num2str(steiner) ' Steiner points had to be included'])
1224	error('Steiner point not supported yet');
1225	end
1226
1227	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1228
1229	md.mesh.elements=elements;
1230	md.mesh.numberofelements=size(elements,1);
1231
1232	%p and q (same deal, except for element that are on the bedrock: )
1233	if ~isnan(md.friction.p),
1234	md.friction.p=md.friction.p(pos_elements);
1235	md.friction.q=md.friction.q(pos_elements);
1236	end
1237
1238	%elementstype
1239	if ~isnan(md.flowequation.element_equation)
1240	oldelements_type=md.flowequation.element_equation;
1241	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1242	end
1243
1244	%connectivity
1245	md.mesh.elementconnectivity=NaN;
1246
1247	%materials
1248	if ~isnan(md.materials.rheology_n),
1249	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1250	end
1251
1252	%increase connectivity if less than 25:
1253	if md.mesh.average_vertex_connectivity<=25,
1254	md.mesh.average_vertex_connectivity=100;
1255	end
1256	end % }}}
1257	function disp(self) % {{{
1258	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
1259	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
1260	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1261	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
1262	disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
1263	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
1264	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
1265	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
1266	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
1267	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
1268	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
1269	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
1270	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
1271	disp(sprintf('%19s: %-22s -- %s','slr' ,['[1x1 ' class(self.slr) ']'],'slr forcings'));
1272	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
1273	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
1274	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
1275	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
1276	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
1277	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
1278	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
1279	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
1280	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
1281	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
1282	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
1283	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
1284	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
1285	disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
1286	disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
1287	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
1288	disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
1289	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
1290	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
1291	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
1292	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
1293	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
1294	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
1295	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
1296	end % }}}
1297	function memory(self) % {{{
1298
1299	disp(sprintf('\nMemory imprint:\n'));
1300
1301	fields=properties('model');
1302	mem=0;
1303
1304	for i=1:length(fields),
1305	field=self.(fields{i});
1306	s=whos('field');
1307	mem=mem+s.bytes/1e6;
1308	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1309	end
1310	disp(sprintf('%19s--%10s','--------------','--------------'));
1311	disp(sprintf('%19s: %g Mb','Total',mem));
1312	end % }}}
1313	function netcdf(self,filename) % {{{
1314	%NETCDF - save model as netcdf
1315	%
1316	% Usage:
1317	% netcdf(md,filename)
1318	%
1319	% Example:
1320	% netcdf(md,'model.nc');
1321
1322	disp('Saving model as NetCDF');
1323	%1. Create NetCDF file
1324	ncid=netcdf.create(filename,'CLOBBER');
1325	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1326	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
1327	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1328	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1329
1330	%Preallocate variable id, needed to write variables in netcdf file
1331	var_id=zeros(1000,1);%preallocate
1332
1333	for step=1:2,
1334	counter=0;
1335	[var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
1336	if step==1, netcdf.endDef(ncid); end
1337	end
1338
1339	if counter>1000,
1340	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1341	end
1342
1343	netcdf.close(ncid)
1344	end % }}}
1345	function xylim(self) % {{{
1346
1347	xlim([min(self.mesh.x) max(self.mesh.x)]);
1348	ylim([min(self.mesh.y) max(self.mesh.y)])
1349	end % }}}
1350	function md=upload(md) % {{{
1351	%the goal of this routine is to upload the model onto a server, and to empty it.
1352	%So first, save the model with a unique name and upload the file to the server:
1353	random_part=fix(rand(1)*10000);
1354	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1355	eval(['save ' id ' md']);
1356
1357	%Now, upload the file:
1358	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1359
1360	%Now, empty this model of everything except settings, and record name of file we just uploaded!
1361	settings_back=md.settings;
1362	md=model();
1363	md.settings=settings_back;
1364	md.settings.upload_filename=id;
1365
1366	%get locally rid of file that was uploaded
1367	eval(['delete ' id]);
1368
1369	end % }}}
1370	function md=download(md) % {{{
1371
1372	%the goal of this routine is to download the internals of the current model from a server, because
1373	%this model is empty, except for the settings which tell us where to go and find this model!
1374
1375	%Download the file:
1376	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1377
1378	name=md.settings.upload_filename;
1379
1380	%Now, load this model:
1381	md=loadmodel(md.settings.upload_filename);
1382
1383	%get locally rid of file that was downloaded
1384	eval(['delete ' name]);
1385
1386	end % }}}
1387	function savemodeljs(md,modelname,websiteroot) % {{{
1388
1389	%the goal of this routine is to save the model as a javascript array that can be included in any html
1390	%file:
1391
1392	%disp:
1393	disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
1394
1395	%open file for writing and declare the model:
1396	fid=fopen([websiteroot '/js/' modelname '.js'],'w');
1397	fprintf(fid,'var %s=new model();\n',modelname);
1398
1399	%now go through all the classes and fwrite all the corresponding fields:
1400
1401	fields=properties('model');
1402	for i=1:length(fields),
1403	field=fields{i};
1404
1405	%Some properties do not need to be saved
1406	if ismember(field,{'results','cluster' }),
1407	continue;
1408	end
1409
1410	%Check that current field is an object
1411	if ~isobject(md.(field))
1412	error(['field ''' char(field) ''' is not an object']);
1413	end
1414
1415	%savemodeljs for current object
1416	%disp(['javascript saving ' field '...']);
1417	savemodeljs(md.(field),fid,modelname);
1418	end
1419
1420	%done, close file:
1421	fclose(fid);
1422	end
1423	end
1424	end

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

Download in other formats: