source: issm/trunk-jpl/src/m/classes/model.m@ 26208

Last change on this file since 26208 was 26208, checked in by schlegel, 4 years ago

CHG: clean up GEMB, change interp_forcings to interp_forcing, isclimatology is now cycle_forcing
File size: 76.4 KB
Line 
1%MODEL class definition
2%
3% Usage:
4% md = model(varargin)
5
6classdef 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 dsl = 0;
25 solidearth = 0;
26
27 debug = 0;
28 verbose = 0;
29 settings = 0;
30 toolkits = 0;
31 cluster = 0;
32
33 balancethickness = 0;
34 stressbalance = 0;
35 groundingline = 0;
36 hydrology = 0;
37 masstransport = 0;
38 thermal = 0;
39 steadystate = 0;
40 transient = 0;
41 levelset = 0;
42 calving = 0;
43 frontalforcings = 0;
44 love = 0;
45 esa = 0;
46 sampling = 0;
47
48 autodiff = 0;
49 inversion = 0;
50 qmu = 0;
51 amr = 0;
52 results = 0;
53 outputdefinition = 0;
54 radaroverlay = 0;
55 miscellaneous = 0;
56 private = 0;
57
58 %}}}
59 end
60 methods (Static)
61 function md = loadobj(md) % {{{
62 % This function is directly called by matlab when a model object is
63 % loaded. If the input is a struct it is an old version of model and
64 % old fields must be recovered (make sure they are in the deprecated
65 % model properties)
66
67 if verLessThan('matlab','7.9'),
68 disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
69 disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
70
71 % This is a Matlab bug: all the fields of md have their default value
72 % Example of error message:
73 % Warning: Error loading an object of class 'model':
74 % Undefined function or method 'exist' for input arguments of type 'cell'
75 %
76 % This has been fixed in MATLAB 7.9 (R2009b) and later versions
77 end
78
79 if isstruct(md)
80 disp('Recovering model object from a previous version');
81 md = structtomodel(model,md);
82 end
83
84 %2012 August 4th
85 if isa(md.materials,'materials'),
86 disp('Recovering old materials');
87 if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
88 md.materials=matice(md.materials);
89 else
90 md.materials=matdamageice(md.materials);
91 end
92 end
93 %2013 April 12
94 if numel(md.stressbalance.loadingforce==1)
95 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
96 end
97 %2013 April 17
98 if isa(md.hydrology,'hydrology'),
99 disp('Recovering old hydrology class');
100 md.hydrology=hydrologyshreve(md.materials);
101 end
102 %2013 October 9
103 if ~isa(md.damage,'damage'),
104 md.damage=damage();
105 md.damage.D=zeros(md.mesh.numberofvertices,1);
106 md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
107 end
108 %2013 November 18
109 if ~isa(md.outputdefinition,'outputdefinition'),
110 md.outputdefinition=outputdefinition();
111 end
112 %2014 March 26th
113 if isa(md.mesh,'mesh'),
114 disp('Recovering old mesh class');
115 if isprop(md.mesh,'dimension'),
116 if md.mesh.dimension==2,
117 md.mesh=mesh2d(md.mesh);
118 else
119 md.mesh=mesh3dprisms(md.mesh);
120 end
121 else
122 md.mesh=mesh2dvertical(md.mesh);
123 end
124 end
125 %2014 November 12
126 if isa(md.calving,'double'); md.calving=calving(); end
127 %2016 October 11
128 if isa(md.esa,'double'); md.esa=esa(); end
129 %2017 February 10th
130 if isa(md.settings,'settings'), %this 'isa' verification: 2018 October 24th
131 if md.settings.solver_residue_threshold==0,
132 md.settings.solver_residue_threshold = 1e-6;
133 end
134 end
135 %2017 May 4th
136 if isa(md.amr,'double'); md.amr=amr(); end
137 %2017 Aug 29th
138 if isa(md.love,'double'); md.love=fourierlove(); end
139 %2017 Oct 26th
140 if isa(md.calving,'calvingdev')
141 disp('Warning: calvingdev is now calvingvonmises');
142 md.calving=calvingvonmises(md.calving);
143 end
144 %2017 Dec 21st (needs to be here)
145 if isempty(md.settings)
146 disp('Warning: md.settings had to be reset, make sure to adjust md.settings.output_frequency and other fields');
147 md.settings = issmsettings();
148 end
149 %2018 Dec 1st
150 if md.settings.sb_coupling_frequency==0
151 md.settings.sb_coupling_frequency=1;
152 end
153 %2019 Jan..
154 if isa(md.frontalforcings,'double');
155 if(isprop('meltingrate',md.calving) & ~isnan(md.calving.meltingrate))
156 gia disp('Warning: md.calving.meltingrate is now in md.frontalforcings');
157 end
158 md.frontalforcings=frontalforcings(md.calving);
159 end
160 %2019 Feb 26
161 if isa(md.settings.results_on_nodes,'double')
162 if md.settings.results_on_nodes == 0
163 md.settings.results_on_nodes = {};
164 else
165 md.settings.results_on_nodes = {'all'};
166 end
167 end
168 %2019 Mar 28, updated 2021 April 23
169 if isa(md.smb,'SMBcomponents') | isa(md.smb,'SMBmeltcomponents') | isa(md.smb,'SMBforcing') | isa(md.smb,'SMBgemb')
170 if isa(md.smb.isclimatology,'double')
171 if prod(size(md.smb.isclimatology)) ~= 1
172 md.smb.isclimatology = 0;
173 end
174 md.timestepping.cycle_forcing=md.smb.isclimatology;
175 end
176 end
177 %2019 Dec 16
178 if isa(md.dsl,'double')
179 md.dsl=dsl();
180 end
181 %2020 April 24
182 if isa(md.smb,'SMBgemb')
183 if isa(md.smb.isconstrainsurfaceT,'double')
184 if prod(size(md.smb.isconstrainsurfaceT)) ~= 1
185 md.smb.isconstrainsurfaceT = 0;
186 end
187 end
188 end
189 %2021 February 17
190 if isa(md.sampling,'double'); md.sampling=sampling(); end
191 end% }}}
192 end
193 methods
194 function md = model(varargin) % {{{
195
196 switch nargin
197 case 0
198 md=setdefaultparameters(md,'earth');
199 otherwise
200 options=pairoptions(varargin{:});
201 planet=getfieldvalue(options,'planet','earth');
202 md=setdefaultparameters(md,planet);
203 end
204
205 end
206 %}}}
207 function md = setdefaultparameters(md,planet) % {{{
208
209 %initialize subclasses
210 md.mesh = mesh2d();
211 md.mask = mask();
212 md.constants = constants();
213 md.geometry = geometry();
214 md.initialization = initialization();
215 md.smb = SMBforcing();
216 md.basalforcings = basalforcings();
217 md.friction = friction();
218 md.rifts = rifts();
219 md.solidearth = solidearth(planet);
220 md.dsl = dsl();
221 md.timestepping = timestepping();
222 md.groundingline = groundingline();
223 md.materials = matice();
224 md.damage = damage();
225 md.flowequation = flowequation();
226 md.debug = debug();
227 md.verbose = verbose();
228 md.settings = issmsettings();
229 md.toolkits = toolkits();
230 md.cluster = generic();
231 md.balancethickness = balancethickness();
232 md.stressbalance = stressbalance();
233 md.hydrology = hydrologyshreve();
234 md.masstransport = masstransport();
235 md.thermal = thermal();
236 md.steadystate = steadystate();
237 md.transient = transient();
238 md.levelset = levelset();
239 md.calving = calving();
240 md.frontalforcings = frontalforcings();
241 md.love = fourierlove();
242 md.esa = esa();
243 md.sampling = sampling();
244 md.autodiff = autodiff();
245 md.inversion = inversion();
246 md.qmu = qmu();
247 md.amr = amr();
248 md.radaroverlay = radaroverlay();
249 md.results = struct();
250 md.outputdefinition = outputdefinition();
251 md.miscellaneous = miscellaneous();
252 md.private = private();
253 end
254 %}}}
255 function md = checkmessage(md,string) % {{{
256 if(nargout~=1) error('wrong usage, model must be an output'); end
257 disp(['model not consistent: ' string]);
258 md.private.isconsistent=false;
259 end
260 %}}}
261 function md = collapse(md)% {{{
262 %COLLAPSE - collapses a 3d mesh into a 2d mesh
263 %
264 % This routine collapses a 3d model into a 2d model
265 % and collapses all the fields of the 3d model by
266 % taking their depth-averaged values
267 %
268 % Usage:
269 % md=collapse(md)
270 %
271 % See also: EXTRUDE, MODELEXTRACT
272
273 %Check that the model is really a 3d model
274 if ~strcmp(md.mesh.elementtype(),'Penta'),
275 error('collapse error message: only 3d mesh can be collapsed')
276 end
277
278 %Start with changing all the fields from the 3d mesh
279
280 %dealing with the friction law
281 %drag is limited to nodes that are on the bedrock.
282 if isa(md.friction,'friction'),
283 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
284 md.friction.p=project2d(md,md.friction.p,1);
285 md.friction.q=project2d(md,md.friction.q,1);
286 elseif isa(md.friction,'frictioncoulomb'),
287 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
288 md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1);
289 md.friction.p=project2d(md,md.friction.p,1);
290 md.friction.q=project2d(md,md.friction.q,1);
291 elseif isa(md.friction,'frictionhydro'),
292 md.friction.q=project2d(md,md.friction.q,1);
293 md.friction.C=project2d(md,md.friction.C,1);
294 md.friction.As=project2d(md,md.friction.As,1);
295 md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
296 elseif isa(md.friction,'frictionwaterlayer'),
297 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
298 md.friction.p=project2d(md,md.friction.p,1);
299 md.friction.q=project2d(md,md.friction.q,1);
300 md.friction.water_layer=project2d(md,md.friction.water_layer,1);
301 elseif isa(md.friction,'frictionweertman'),
302 md.friction.C=project2d(md,md.friction.C,1);
303 md.friction.m=project2d(md,md.friction.m,1);
304 elseif isa(md.friction,'frictionweertmantemp'),
305 md.friction.C=project2d(md,md.friction.C,1);
306 md.friction.m=project2d(md,md.friction.m,1);
307 elseif isa(md.friction,'frictionjosh'),
308 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
309 md.friction.pressure_adjusted_temperature=project2d(md,md.friction.pressure_adjusted_temperature,1);
310 else
311 disp('friction type not supported');
312 end
313
314 %observations
315 if ~isnan(md.inversion.vx_obs),
316 md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers);
317 end
318 if ~isnan(md.inversion.vy_obs),
319 md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers);
320 end
321 if ~isnan(md.inversion.vel_obs),
322 md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers);
323 end
324 if ~isnan(md.inversion.thickness_obs),
325 md.inversion.thickness_obs=project2d(md,md.inversion.thickness_obs,md.mesh.numberoflayers);
326 end
327 if ~isnan(md.inversion.cost_functions_coefficients),
328 md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers);
329 end
330 if numel(md.inversion.min_parameters)>1,
331 md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers);
332 end
333 if numel(md.inversion.max_parameters)>1,
334 md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers);
335 end
336 if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
337 md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
338 elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
339 md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
340 end
341
342 %results
343 if ~isnan(md.initialization.vx),
344 md.initialization.vx=DepthAverage(md,md.initialization.vx);
345 end
346 if ~isnan(md.initialization.vy),
347 md.initialization.vy=DepthAverage(md,md.initialization.vy);
348 end
349 if ~isnan(md.initialization.vz),
350 md.initialization.vz=DepthAverage(md,md.initialization.vz);
351 end
352 if ~isnan(md.initialization.vel),
353 md.initialization.vel=DepthAverage(md,md.initialization.vel);
354 end
355 if ~isnan(md.initialization.temperature),
356 md.initialization.temperature=DepthAverage(md,md.initialization.temperature);
357 end
358 if ~isnan(md.initialization.pressure),
359 md.initialization.pressure=project2d(md,md.initialization.pressure,1);
360 end
361 if ~isnan(md.initialization.sediment_head),
362 md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);
363 end
364 if ~isnan(md.initialization.epl_head),
365 md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);
366 end
367 if ~isnan(md.initialization.epl_thickness),
368 md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);
369 end
370 if ~isnan(md.initialization.waterfraction),
371 md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);
372 end
373 if ~isnan(md.initialization.watercolumn),
374 md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);
375 end
376
377
378 %elementstype
379 if ~isnan(md.flowequation.element_equation)
380 md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
381 md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
382 md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
383 md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
384 md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
385 end
386
387 %boundary conditions
388 md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
389 md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
390 md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
391 md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
392 md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
393 if numel(md.masstransport.spcthickness)>1,
394 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
395 end
396 if numel(md.damage.spcdamage)>1,
397 md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers);
398 end
399 if numel(md.levelset.spclevelset)>1,
400 md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers);
401 end
402 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
403
404 % Hydrologydc variables
405 if isa(md.hydrology,'hydrologydc');
406 md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
407 md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
408 md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
409 md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
410 if(md.hydrology.isefficientlayer==1)
411 md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
412 end
413 end
414
415 %materials
416 md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
417 md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
418
419 %damage:
420 if md.damage.isdamage,
421 md.damage.D=DepthAverage(md,md.damage.D);
422 end
423
424 %special for thermal modeling:
425 if ~isnan(md.basalforcings.groundedice_melting_rate),
426 md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
427 end
428 if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
429 md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
430 end
431 md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
432
433 if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
434 md.calving.coeff=project2d(md,md.calving.coeff,1);
435 end
436 if isprop(md.frontalforcings,'meltingrate') & ~isnan(md.frontalforcings.meltingrate),
437 md.frontalforcings.meltingrate=project2d(md,md.frontalforcings.meltingrate,1);
438 end
439
440 %update of connectivity matrix
441 md.mesh.average_vertex_connectivity=25;
442
443 %Collapse the mesh
444 nodes2d=md.mesh.numberofvertices2d;
445 elements2d=md.mesh.numberofelements2d;
446
447 %parameters
448 md.geometry.surface=project2d(md,md.geometry.surface,1);
449 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
450 md.geometry.base=project2d(md,md.geometry.base,1);
451 if ~isnan(md.geometry.bed),
452 md.geometry.bed=project2d(md,md.geometry.bed,1);
453 end
454 if ~isnan(md.mask.ocean_levelset),
455 md.mask.ocean_levelset=project2d(md,md.mask.ocean_levelset,1);
456 end
457 if ~isnan(md.mask.ice_levelset),
458 md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
459 end
460
461 %lat long
462 if numel(md.mesh.lat)==md.mesh.numberofvertices,
463 md.mesh.lat=project2d(md,md.mesh.lat,1);
464 end
465 if numel(md.mesh.long)==md.mesh.numberofvertices,
466 md.mesh.long=project2d(md,md.mesh.long,1);
467 end
468
469 %outputdefinitions
470 for i=1:length(md.outputdefinition.definitions)
471 if isobject(md.outputdefinition.definitions{i})
472 %get subfields
473 solutionsubfields=fields(md.outputdefinition.definitions{i});
474 for j=1:length(solutionsubfields),
475 field=md.outputdefinition.definitions{i}.(solutionsubfields{j});
476 if length(field)==md.mesh.numberofvertices | length(field)==md.mesh.numberofelements,
477 md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1);
478 end
479 end
480 end
481 end
482
483 %Initialize the 2d mesh
484 mesh=mesh2d();
485 mesh.x=md.mesh.x2d;
486 mesh.y=md.mesh.y2d;
487 mesh.numberofvertices=md.mesh.numberofvertices2d;
488 mesh.numberofelements=md.mesh.numberofelements2d;
489 mesh.elements=md.mesh.elements2d;
490 if numel(md.mesh.lat)==md.mesh.numberofvertices,
491 mesh.lat=project2d(md,md.mesh.lat,1);
492 end
493 if numel(md.mesh.long)==md.mesh.numberofvertices,
494 mesh.long=project2d(md,md.mesh.long,1);
495 end
496 mesh.epsg=md.mesh.epsg;
497 if numel(md.mesh.scale_factor)==md.mesh.numberofvertices,
498 mesh.scale_factor=project2d(md,md.mesh.scale_factor,1);
499 end
500 if ~isnan(md.mesh.vertexonboundary),
501 mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
502 end
503 if ~isnan(md.mesh.elementconnectivity),
504 mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
505 end
506 md.mesh=mesh;
507 md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
508 md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
509 md.mesh.segments=contourenvelope(md.mesh);
510
511 end % }}}
512 function md2 = extract(md,area,varargin) % {{{
513 %extract - extract a model according to an Argus contour or flag list
514 %
515 % This routine extracts a submodel from a bigger model with respect to a given contour
516 % md must be followed by the corresponding exp file or flags list
517 % It can either be a domain file (argus type, .exp extension), or an array of element flags.
518 % If user wants every element outside the domain to be
519 % extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
520 % an empty string '' will be considered as an empty domain
521 % a string 'all' will be considered as the entire domain
522 %
523 % Usage:
524 % md2=extract(md,area);
525 %
526 % Examples:
527 % md2=extract(md,'Domain.exp');
528 %
529 % See also: EXTRUDE, COLLAPSE
530
531 %copy model
532 md1=md;
533
534 %recover optoins:
535 options=pairoptions(varargin{:});
536
537 %some checks
538 if ((nargin<2) | (nargout~=1)),
539 help extract
540 error('extract error message: bad usage');
541 end
542
543 %get elements that are inside area
544 flag_elem=FlagElements(md1,area);
545 if ~any(flag_elem),
546 error('extracted model is empty');
547 end
548
549 %kick out all elements with 3 dirichlets
550 if getfieldvalue(options,'spccheck',1)
551 spc_elem=find(~flag_elem);
552 spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
553 flag=ones(md1.mesh.numberofvertices,1);
554 flag(spc_node)=0;
555 pos=find(sum(flag(md1.mesh.elements),2)==0);
556 flag_elem(pos)=0;
557 end
558
559 %extracted elements and nodes lists
560 pos_elem=find(flag_elem);
561 pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
562
563 %keep track of some fields
564 numberofvertices1=md1.mesh.numberofvertices;
565 numberofelements1=md1.mesh.numberofelements;
566 numberofvertices2=length(pos_node);
567 numberofelements2=length(pos_elem);
568 flag_node=zeros(numberofvertices1,1);
569 flag_node(pos_node)=1;
570
571 %Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
572 Pelem=zeros(numberofelements1,1);
573 Pelem(pos_elem)=[1:numberofelements2]';
574 Pnode=zeros(numberofvertices1,1);
575 Pnode(pos_node)=[1:numberofvertices2]';
576
577 %renumber the elements (some nodes won't exist anymore)
578 elements_1=md1.mesh.elements;
579 elements_2=elements_1(pos_elem,:);
580 elements_2(:,1)=Pnode(elements_2(:,1));
581 elements_2(:,2)=Pnode(elements_2(:,2));
582 elements_2(:,3)=Pnode(elements_2(:,3));
583 if isa(md1.mesh,'mesh3dprisms'),
584 elements_2(:,4)=Pnode(elements_2(:,4));
585 elements_2(:,5)=Pnode(elements_2(:,5));
586 elements_2(:,6)=Pnode(elements_2(:,6));
587 end
588
589 %OK, now create the new model!
590
591 %take every field from model
592 md2=md1;
593
594 %automatically modify fields
595
596 %loop over model fields
597 model_fields=fields(md1);
598 for i=1:length(model_fields),
599 %get field
600 field=md1.(model_fields{i});
601 fieldsize=size(field);
602 if isobject(field), %recursive call
603 object_fields=fields(md1.(model_fields{i}));
604 for j=1:length(object_fields),
605 %get field
606 field=md1.(model_fields{i}).(object_fields{j});
607 fieldsize=size(field);
608 %size = number of nodes * n
609 if fieldsize(1)==numberofvertices1
610 md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
611 elseif (fieldsize(1)==numberofvertices1+1)
612 md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
613 %size = number of elements * n
614 elseif fieldsize(1)==numberofelements1
615 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
616 elseif (fieldsize(1)==numberofelements1+1)
617 md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
618 end
619 end
620 else
621 %size = number of nodes * n
622 if fieldsize(1)==numberofvertices1
623 md2.(model_fields{i})=field(pos_node,:);
624 elseif (fieldsize(1)==numberofvertices1+1)
625 md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
626 %size = number of elements * n
627 elseif fieldsize(1)==numberofelements1
628 md2.(model_fields{i})=field(pos_elem,:);
629 elseif (fieldsize(1)==numberofelements1+1)
630 md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
631 end
632 end
633 end
634
635 %modify some specific fields
636
637 %Mesh
638 md2.mesh.numberofelements=numberofelements2;
639 md2.mesh.numberofvertices=numberofvertices2;
640 md2.mesh.elements=elements_2;
641
642 %mesh.uppervertex mesh.lowervertex
643 if isa(md1.mesh,'mesh3dprisms'),
644 md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
645 pos=find(~isnan(md2.mesh.uppervertex));
646 md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
647
648 md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
649 pos=find(~isnan(md2.mesh.lowervertex));
650 md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
651
652 md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
653 pos=find(~isnan(md2.mesh.upperelements));
654 md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
655
656 md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
657 pos=find(~isnan(md2.mesh.lowerelements));
658 md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
659 end
660
661 %Initial 2d mesh
662 if isa(md1.mesh,'mesh3dprisms'),
663 flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
664 pos_elem_2d=find(flag_elem_2d);
665 flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
666 pos_node_2d=find(flag_node_2d);
667
668 md2.mesh.numberofelements2d=length(pos_elem_2d);
669 md2.mesh.numberofvertices2d=length(pos_node_2d);
670 md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
671 md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
672 md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
673 md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
674
675 md2.mesh.x2d=md1.mesh.x(pos_node_2d);
676 md2.mesh.y2d=md1.mesh.y(pos_node_2d);
677 end
678
679 %Edges
680 if(dimension(md.mesh)==2),
681 if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
682 %renumber first two columns
683 pos=find(md2.mesh.edges(:,4)~=-1);
684 md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
685 md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
686 md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
687 md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
688 %remove edges when the 2 vertices are not in the domain.
689 md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
690 %Replace all zeros by -1 in the last two columns
691 pos=find(md2.mesh.edges(:,3)==0);
692 md2.mesh.edges(pos,3)=-1;
693 pos=find(md2.mesh.edges(:,4)==0);
694 md2.mesh.edges(pos,4)=-1;
695 %Invert -1 on the third column with last column (Also invert first two columns!!)
696 pos=find(md2.mesh.edges(:,3)==-1);
697 md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
698 md2.mesh.edges(pos,4)=-1;
699 values=md2.mesh.edges(pos,2);
700 md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
701 md2.mesh.edges(pos,1)=values;
702 %Finally remove edges that do not belong to any element
703 pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
704 md2.mesh.edges(pos,:)=[];
705 end
706 end
707
708 %Penalties
709 if ~isnan(md2.stressbalance.vertex_pairing),
710 for i=1:size(md1.stressbalance.vertex_pairing,1);
711 md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
712 end
713 md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
714 end
715 if ~isnan(md2.masstransport.vertex_pairing),
716 for i=1:size(md1.masstransport.vertex_pairing,1);
717 md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
718 end
719 md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
720 end
721
722 %recreate segments
723 if isa(md1.mesh,'mesh2d') | isa(md1.mesh','mesh3dsurface'),
724 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
725 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
726 md2.mesh.segments=contourenvelope(md2.mesh);
727 md2.mesh.vertexonboundary=zeros(numberofvertices2,1);
728 md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
729 else
730 %First do the connectivity for the contourenvelope in 2d
731 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
732 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
733 segments=contourenvelope(md2.mesh);
734 md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1);
735 md2.mesh.vertexonboundary(segments(:,1:2))=1;
736 md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
737 %Then do it for 3d as usual
738 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
739 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
740 end
741
742 %Boundary conditions: Dirichlets on new boundary
743 %Catch the elements that have not been extracted
744 orphans_elem=find(~flag_elem);
745 orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
746 %Figure out which node are on the boundary between md2 and md1
747 nodestoflag1=intersect(orphans_node,pos_node);
748 nodestoflag2=Pnode(nodestoflag1);
749 if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>1 & numel(md1.stressbalance.spcvz)>1,
750 if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
751 md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
752 md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
753 else
754 md2.stressbalance.spcvx(nodestoflag2)=NaN;
755 md2.stressbalance.spcvy(nodestoflag2)=NaN;
756 disp(' ')
757 disp('!! extract warning: spc values should be checked !!')
758 disp(' ')
759 end
760 %put 0 for vz
761 md2.stressbalance.spcvz(nodestoflag2)=0;
762 end
763 if ~isnan(md1.thermal.spctemperature),
764 md2.thermal.spctemperature(nodestoflag2,1)=1;
765 end
766
767 %Results fields
768 if isstruct(md1.results),
769 md2.results=struct();
770 solutionfields=fields(md1.results);
771 for i=1:length(solutionfields),
772 if isstruct(md1.results.(solutionfields{i}))
773 %get subfields
774 % loop over time steps
775 for p=1:length(md1.results.(solutionfields{i}))
776 current = md1.results.(solutionfields{i})(p);
777 solutionsubfields=fields(current);
778 for j=1:length(solutionsubfields),
779 field=md1.results.(solutionfields{i})(p).(solutionsubfields{j});
780 if length(field)==numberofvertices1,
781 md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_node);
782 elseif length(field)==numberofelements1,
783 md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_elem);
784 else
785 md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field;
786 end
787 end
788 end
789 else
790 field=md1.results.(solutionfields{i});
791 if length(field)==numberofvertices1,
792 md2.results.(solutionfields{i})=field(pos_node);
793 elseif length(field)==numberofelements1,
794 md2.results.(solutionfields{i})=field(pos_elem);
795 else
796 md2.results.(solutionfields{i})=field;
797 end
798 end
799 end
800 end
801
802 %OutputDefinitions fields
803 for i=1:length(md1.outputdefinition.definitions),
804 if isobject(md1.outputdefinition.definitions{i})
805 %get subfields
806 solutionsubfields=fields(md1.outputdefinition.definitions{i});
807 for j=1:length(solutionsubfields),
808 field=md1.outputdefinition.definitions{i}.(solutionsubfields{j});
809 if length(field)==numberofvertices1,
810 md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node);
811 elseif length(field)==numberofelements1,
812 md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem);
813 end
814 end
815 end
816 end
817
818 %Keep track of pos_node and pos_elem
819 md2.mesh.extractedvertices=pos_node;
820 md2.mesh.extractedelements=pos_elem;
821 end % }}}
822 function md2 = refine(md) % {{{
823 %refine - split all triangles into 3 to refine the mesh everywhere
824 %
825 % This function only works for 2d triangle meshes
826 %
827 % Usage:
828 % md2=refine(md);
829 %
830 % See also: EXTRUDE, COLLAPSE, EXTRACT
831
832 %Check incoming
833 if ~strcmp(elementtype(md.mesh),'Tria')
834 error('not supported for 3d meshes');
835 end
836
837 %copy model
838 md2=md;
839
840 disp('Getting edges');
841 %initialization of some variables
842 nbe = md.mesh.numberofelements;
843 nbv = md.mesh.numberofvertices;
844 index = md.mesh.elements;
845 elementslist=1:nbe;
846 %1: list of edges
847 edges=[index(:,[1,2]); index(:,[2,3]); index(:,[3,1])];
848 %2: find unique edges
849 [edges,I,J]=unique(sort(edges,2),'rows');
850 %3: unique edge numbers
851 vec=J;
852 %4: unique edges numbers in each triangle (2 triangles sharing the same edge will have the same edge number)
853 edges_tria=[vec(elementslist+nbe) vec(elementslist+2*nbe) vec(elementslist)];
854
855 % We divide each element as follows
856 %
857 % e2
858 % n1 ------------+------------ n3
859 % \ / \ /
860 % \ 1 / \ 3 /
861 % \ / \ /
862 % \ / 2 \ /
863 % \ / \ /
864 % e3 +____________\/ e1
865 % \ /
866 % \ /
867 % \ 4 /
868 % \ /
869 % \ /
870 % n2
871
872 %Create new coordinates
873 disp('Remeshing...');
874 x_edges = 0.5*(md.mesh.x(edges(:,1)) + md.mesh.x(edges(:,2)));
875 y_edges = 0.5*(md.mesh.y(edges(:,1)) + md.mesh.y(edges(:,2)));
876 md2.mesh.x = [md2.mesh.x;x_edges];
877 md2.mesh.y = [md2.mesh.y;y_edges];
878 md2.mesh.elements = [...
879 index(:,1) nbv+edges_tria(:,3) nbv+edges_tria(:,2);...
880 nbv+edges_tria(:,2) nbv+edges_tria(:,3) nbv+edges_tria(:,1);...
881 nbv+edges_tria(:,2) nbv+edges_tria(:,1) index(:,3);...
882 nbv+edges_tria(:,3) index(:,2) nbv+edges_tria(:,1)];
883 md2.mesh.numberofelements = 4*nbe;
884 md2.mesh.numberofvertices = nbv + size(edges,1);
885 disp([' Old number of elements: ' num2str(nbe)]);
886 disp([' New number of elements: ' num2str(4*nbe)]);
887
888 disp('Interpolate all fields');
889 numberofvertices1 = md.mesh.numberofvertices;
890 numberofelements1 = md.mesh.numberofelements;
891 nbv2 = md2.mesh.numberofvertices;
892 %Create transformation vectors
893 nbedges = size(edges,1);
894 Pelem = sparse(1:4*nbe,repmat([1:nbe],1,4),ones(4*nbe,1),4*nbe,nbe);
895 Pnode = sparse([1:nbv,repmat([nbv+1:nbv+nbedges],1,2)],[1:nbv edges(:)'],[ones(nbv,1);1/2*ones(2*nbedges,1)],md2.mesh.numberofvertices,nbv);
896 %loop over model fields
897 model_fields=setxor(fields(md),{'mesh'});
898 %remove mesh from this field
899 for i=1:length(model_fields),
900 %get field
901 field=md.(model_fields{i});
902 fieldsize=size(field);
903 if isobject(field), %recursive call
904 object_fields=fields(md.(model_fields{i}));
905 for j=1:length(object_fields),
906 %get field
907 field=md.(model_fields{i}).(object_fields{j});
908 fieldsize=size(field);
909 %size = number of nodes * n
910 if fieldsize(1)==numberofvertices1
911 md2.(model_fields{i}).(object_fields{j})=Pnode*field;
912 elseif (fieldsize(1)==numberofvertices1+1)
913 md2.(model_fields{i}).(object_fields{j})=[Pnode*field(1:end-1,:); field(end,:)];
914 %size = number of elements * n
915 elseif fieldsize(1)==numberofelements1
916 md2.(model_fields{i}).(object_fields{j})=Pelem*field;
917 elseif (fieldsize(1)==numberofelements1+1)
918 md2.(model_fields{i}).(object_fields{j})=[Pelem*field(1:end-1,:); field(end,:)];
919 end
920 end
921 else
922 %size = number of nodes * n
923 if fieldsize(1)==numberofvertices1
924 md2.(model_fields{i})=Pnode*field;
925 elseif (fieldsize(1)==numberofvertices1+1)
926 md2.(model_fields{i})=[Pnode*field(1:end-1,:); field(end,:)];
927 %size = number of elements * n
928 elseif fieldsize(1)==numberofelements1
929 md2.(model_fields{i})=Pelem*field;
930 elseif (fieldsize(1)==numberofelements1+1)
931 md2.(model_fields{i})=[Pelem*field(1:end-1,:); field(end,:)];
932 end
933 end
934 end
935
936 end % }}}
937 function md = extrude(md,varargin) % {{{
938 %EXTRUDE - vertically extrude a 2d mesh
939 %
940 % vertically extrude a 2d mesh and create corresponding 3d mesh.
941 % The vertical distribution can:
942 % - follow a polynomial law
943 % - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
944 % - be discribed by a list of coefficients (between 0 and 1)
945 %
946 %
947 % Usage:
948 % md=extrude(md,numlayers,extrusionexponent);
949 % md=extrude(md,numlayers,lowerexponent,upperexponent);
950 % md=extrude(md,listofcoefficients);
951 %
952 % Example:
953 % md=extrude(md,15,1.3);
954 % md=extrude(md,15,1.3,1.2);
955 % md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
956 %
957 % See also: MODELEXTRACT, COLLAPSE
958
959 %some checks on list of arguments
960 if ((nargin>4) | (nargin<2) | (nargout~=1)),
961 help extrude;
962 error('extrude error message');
963 end
964 if numel(md.geometry.base)~=md.mesh.numberofvertices || numel(md.geometry.surface)~=md.mesh.numberofvertices
965 error('model has not been parameterized yet: base and/or surface not set');
966 end
967
968 %Extrude the mesh
969 if nargin==2, %list of coefficients
970 clist=varargin{1};
971 if any(clist<0) | any(clist>1),
972 error('extrusioncoefficients must be between 0 and 1');
973 end
974 extrusionlist=sort(unique([clist(:);0;1]));
975 numlayers=length(extrusionlist);
976 elseif nargin==3, %one polynomial law
977 if varargin{2}<=0,
978 help extrude;
979 error('extrusionexponent must be >=0');
980 end
981 numlayers=varargin{1};
982 extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
983 elseif nargin==4, %two polynomial laws
984 numlayers=varargin{1};
985 lowerexp=varargin{2};
986 upperexp=varargin{3};
987
988 if varargin{2}<=0 | varargin{3}<=0,
989 help extrude;
990 error('lower and upper extrusionexponents must be >=0');
991 end
992
993 lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
994 upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
995 extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
996
997 end
998
999 if numlayers<2,
1000 error('number of layers should be at least 2');
1001 end
1002 if strcmp(md.mesh.domaintype(),'3D')
1003 error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
1004 end
1005
1006 %Initialize with the 2d mesh
1007 mesh2d = md.mesh;
1008 md.mesh=mesh3dprisms();
1009 md.mesh.x = mesh2d.x;
1010 md.mesh.y = mesh2d.y;
1011 md.mesh.elements = mesh2d.elements;
1012 md.mesh.numberofelements = mesh2d.numberofelements;
1013 md.mesh.numberofvertices = mesh2d.numberofvertices;
1014
1015 md.mesh.lat = mesh2d.lat;
1016 md.mesh.long = mesh2d.long;
1017 md.mesh.epsg = mesh2d.epsg;
1018 md.mesh.scale_factor = mesh2d.scale_factor;
1019
1020 md.mesh.vertexonboundary = mesh2d.vertexonboundary;
1021 md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
1022 md.mesh.elementconnectivity = mesh2d.elementconnectivity;
1023 md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
1024
1025 md.mesh.extractedvertices = mesh2d.extractedvertices;
1026 md.mesh.extractedelements = mesh2d.extractedelements;
1027
1028 x3d=[];
1029 y3d=[];
1030 z3d=[]; %the lower node is on the bed
1031 thickness3d=md.geometry.thickness; %thickness and bed for these nodes
1032 bed3d=md.geometry.base;
1033
1034 %Create the new layers
1035 for i=1:numlayers,
1036 x3d=[x3d; md.mesh.x];
1037 y3d=[y3d; md.mesh.y];
1038 %nodes are distributed between bed and surface accordingly to the given exponent
1039 z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
1040 end
1041 number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
1042
1043 %Extrude elements
1044 elements3d=[];
1045 for i=1:numlayers-1,
1046 elements3d=[elements3d;[md.mesh.elements+(i-1)*md.mesh.numberofvertices md.mesh.elements+i*md.mesh.numberofvertices]]; %Create the elements of the 3d mesh for the non extruded part
1047 end
1048 number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
1049
1050 %Keep a trace of lower and upper nodes
1051 lowervertex=NaN*ones(number_nodes3d,1);
1052 uppervertex=NaN*ones(number_nodes3d,1);
1053 lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
1054 uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
1055 md.mesh.lowervertex=lowervertex;
1056 md.mesh.uppervertex=uppervertex;
1057
1058 %same for lower and upper elements
1059 lowerelements=NaN*ones(number_el3d,1);
1060 upperelements=NaN*ones(number_el3d,1);
1061 lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
1062 upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
1063 md.mesh.lowerelements=lowerelements;
1064 md.mesh.upperelements=upperelements;
1065
1066 %Save old mesh
1067 md.mesh.x2d=md.mesh.x;
1068 md.mesh.y2d=md.mesh.y;
1069 md.mesh.elements2d=md.mesh.elements;
1070 md.mesh.numberofelements2d=md.mesh.numberofelements;
1071 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
1072
1073 %Build global 3d mesh
1074 md.mesh.elements=elements3d;
1075 md.mesh.x=x3d;
1076 md.mesh.y=y3d;
1077 md.mesh.z=z3d;
1078 md.mesh.numberofelements=number_el3d;
1079 md.mesh.numberofvertices=number_nodes3d;
1080 md.mesh.numberoflayers=numlayers;
1081
1082 %Ok, now deal with the other fields from the 2d mesh:
1083
1084 %bedinfo and surface info
1085 md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
1086 md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
1087 md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
1088
1089 %lat long
1090 md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
1091 md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
1092 md.mesh.scale_factor=project3d(md,'vector',md.mesh.scale_factor,'type','node');
1093
1094 md.geometry=extrude(md.geometry,md);
1095 md.friction = extrude(md.friction,md);
1096 md.inversion = extrude(md.inversion,md);
1097 md.smb = extrude(md.smb,md);
1098 md.initialization = extrude(md.initialization,md);
1099
1100 md.flowequation=md.flowequation.extrude(md);
1101 md.stressbalance=extrude(md.stressbalance,md);
1102 md.thermal=md.thermal.extrude(md);
1103 md.masstransport=md.masstransport.extrude(md);
1104 md.levelset=extrude(md.levelset,md);
1105 md.calving=extrude(md.calving,md);
1106 md.frontalforcings=extrude(md.frontalforcings,md);
1107 md.hydrology = extrude(md.hydrology,md);
1108 md.solidearth = extrude(md.solidearth,md);
1109 md.dsl = extrude(md.dsl,md);
1110
1111 %connectivity
1112 if ~isnan(md.mesh.elementconnectivity)
1113 md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
1114 md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
1115 for i=2:numlayers-1,
1116 md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
1117 =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
1118 end
1119 md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
1120 end
1121
1122 md.materials=extrude(md.materials,md);
1123 md.damage=extrude(md.damage,md);
1124 md.mask=extrude(md.mask,md);
1125 md.qmu=extrude(md.qmu,md);
1126 md.basalforcings=extrude(md.basalforcings,md);
1127 md.outputdefinition=extrude(md.outputdefinition,md);
1128
1129 %increase connectivity if less than 25:
1130 if md.mesh.average_vertex_connectivity<=25,
1131 md.mesh.average_vertex_connectivity=100;
1132 end
1133 end % }}}
1134 function md = structtomodel(md,structmd) % {{{
1135
1136 if ~isstruct(structmd) error('input model is not a structure'); end
1137
1138 %loaded model is a struct, initialize output and recover all fields
1139 md = structtoobj(model,structmd);
1140
1141 %Old field now classes
1142 if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
1143 if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
1144
1145 %Field name change
1146 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
1147 if isfield(structmd,'p'), md.friction.p=structmd.p; end
1148 if isfield(structmd,'q'), md.friction.q=structmd.p; end
1149 if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
1150 if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
1151 if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
1152 if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
1153 if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
1154 if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
1155 if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
1156 if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
1157 if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
1158 if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
1159 if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
1160 if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
1161 if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
1162 if isfield(structmd,'g'), md.constants.g=structmd.g; end
1163 if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
1164 if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
1165 if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
1166 if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
1167 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
1168 if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
1169 if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
1170 if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
1171 if isfield(structmd,'riftproperties'), %old implementation
1172 md.rifts=rifts();
1173 md.rifts.riftproperties=structmd.riftproperties;
1174 md.rifts.riftstruct=structmd.rifts;
1175 md.rifts.riftproperties=structmd.riftinfo;
1176 end
1177 if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
1178 if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
1179 if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
1180 if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
1181 if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
1182 if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
1183 if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
1184 if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
1185 if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
1186 if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
1187 if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
1188 if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
1189 if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
1190 if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
1191 if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
1192 if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
1193 if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
1194 if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
1195 if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
1196 if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
1197 if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
1198 if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
1199 if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
1200 if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
1201 if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
1202 if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
1203 if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
1204 if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
1205 if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
1206 if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
1207 if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
1208 if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
1209 if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
1210 if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
1211 if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
1212 if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
1213 if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
1214 if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
1215 if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
1216 if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
1217 if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
1218 if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
1219 if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
1220 if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
1221 if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
1222 if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
1223 if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
1224 if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
1225 if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
1226 if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
1227 if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
1228 if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
1229 if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
1230 if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
1231 if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
1232 if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
1233 if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
1234 if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
1235 if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
1236 if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
1237 if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
1238 if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
1239 if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
1240 if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
1241 if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
1242 if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
1243 if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
1244 if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
1245 if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
1246 if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
1247 if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
1248 if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
1249 if isfield(structmd,'long'), md.mesh.long=structmd.long; end
1250 if isfield(structmd,'scale_factor'), md.mesh.scale_factor=structmd.scale_factor; end
1251 if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
1252 if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
1253 if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
1254 if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
1255 if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
1256 if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
1257 if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
1258 if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
1259 if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
1260 if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
1261 if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
1262 if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
1263 if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
1264 if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
1265 if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
1266 if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
1267 if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
1268 if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
1269 if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
1270 if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
1271 if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
1272 if isfield(structmd,'edges'),
1273 md.mesh.edges=structmd.edges;
1274 md.mesh.edges(isnan(md.mesh.edges))=-1;
1275 end
1276 if isfield(structmd,'y'), md.mesh.y=structmd.y; end
1277 if isfield(structmd,'x'), md.mesh.x=structmd.x; end
1278 if isfield(structmd,'z'), md.mesh.z=structmd.z; end
1279 if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
1280 if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
1281 if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
1282
1283 if isnumeric(md.verbose),
1284 md.verbose=verbose;
1285 end
1286
1287 if isfield(structmd,'spcvelocity'),
1288 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
1289 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
1290 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1291 pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
1292 pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
1293 pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
1294 end
1295 if isfield(structmd,'spcvx'),
1296 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
1297 pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
1298 end
1299 if isfield(structmd,'spcvy'),
1300 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
1301 pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
1302 end
1303 if isfield(structmd,'spcvz'),
1304 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1305 pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
1306 end
1307 if isfield(structmd,'pressureload'),
1308 if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
1309 pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
1310 pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
1311 pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
1312 end
1313 end
1314 if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
1315 pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
1316 pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
1317 pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
1318 pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
1319 pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
1320 pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
1321 pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
1322 pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
1323 end
1324 if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
1325 pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
1326 pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
1327 pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
1328 pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
1329 pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
1330 pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
1331 pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
1332 pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
1333 end
1334 if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
1335 if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
1336 if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1337 if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1338 end
1339 if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1340 if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1341 if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
1342 if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1343 end
1344 if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1345 if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1346 if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1347 if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1348 end
1349 if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1350 pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1351 pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1352 pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1353 pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1354 pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1355 pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1356 pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1357 pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1358 pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1359 end
1360
1361 if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1362 md.thermal.stabilization=2;
1363 md.masstransport.stabilization=1;
1364 md.balancethickness.stabilization=1;
1365 end
1366 if isnumeric(md.masstransport.hydrostatic_adjustment)
1367 if md.masstransport.hydrostatic_adjustment==269,
1368 md.masstransport.hydrostatic_adjustment='Incremental';
1369 else
1370 md.masstransport.hydrostatic_adjustment='Absolute';
1371 end
1372 end
1373
1374 %New fields
1375 if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
1376 md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1377 md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1378 end
1379 if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
1380 md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1381 md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1382 end
1383 if ~isfield(structmd,'diagnostic_ref');
1384 md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1385 end
1386 if ~isfield(structmd,'loadingforce');
1387 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1388 end
1389
1390 %2013 August 9
1391 if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1392 disp('Recovering old prognostic class');
1393 md.masstransport=masstransport(structmd.prognostic);
1394 end
1395 %2013 August 9
1396 if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') || isa(structmd.diagnostic,'stressbalance')),
1397 disp('Recovering old diagnostic class');
1398 md.stressbalance=stressbalance(structmd.diagnostic);
1399 end
1400 %2014 January 9th
1401 if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
1402 disp('Recovering old surfaceforcings class');
1403 mass_balance=structmd.surfaceforcings.mass_balance;
1404 md.smb=SMB();
1405 md.smb.mass_balance=mass_balance;
1406 end
1407 %2015 September 10
1408 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
1409 disp('Recovering old SMB class');
1410 md.smb=SMBforcing(structmd.surfaceforcings);
1411 end
1412 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
1413 disp('Recovering old SMBhenning class');
1414 md.smb=SMBhenning(structmd.surfaceforcings);
1415 end
1416 if isfield(structmd,'slr'),
1417 disp('Recovering old slr class');
1418 if isfield(structmd.slr,'sealevel'),
1419 md.solidearth.sealevel=structmd.slr.sealevel;
1420 end
1421 md.solidearth.planetradius=structmd.slr.planetradius;
1422 md.solidearth.requested_outputs=structmd.slr.requested_outputs;
1423 md.solidearth.transitions=structmd.slr.transitions;
1424
1425 md.solidearth.transitions=structmd.slr.transitions;
1426 md.solidearth.settings.reltol=structmd.slr.reltol;
1427 md.solidearth.settings.abstol=structmd.slr.abstol;
1428 md.solidearth.settings.maxiter=structmd.slr.maxiter;
1429 md.solidearth.settings.rigid=structmd.slr.rigid;
1430 md.solidearth.settings.elastic=structmd.slr.elastic;
1431 md.solidearth.settings.rotation=structmd.slr.rotation;
1432 md.solidearth.settings.runfrequency=structmd.slr.geodetic_run_frequency;
1433 md.solidearth.settings.computesealevelchange=structmd.slr.geodetic;
1434 md.solidearth.settings.degacc=structmd.slr.degacc;
1435 md.solidearth.settings.horiz=structmd.slr.horiz;
1436 md.solidearth.settings.ocean_area_scaling=structmd.slr.ocean_area_scaling;
1437
1438 md.solidearth.surfaceload.icethicknesschange=structmd.slr.deltathickness;
1439 md.solidearth.surfaceload.waterheightchange=structmd.slr.hydro_rate;
1440
1441 md.solidearth.lovenumbers.h=structmd.slr.love_h;
1442 md.solidearth.lovenumbers.k=structmd.slr.love_k;
1443 md.solidearth.lovenumbers.l=structmd.slr.love_l;
1444 md.solidearth.lovenumbers.th=structmd.slr.tide_love_h;
1445 md.solidearth.lovenumbers.tk=structmd.slr.tide_love_k;
1446 md.solidearth.lovenumbers.tk2secular=structmd.slr.fluid_love;
1447
1448 md.solidearth.rotational.equatorialmoi=structmd.slr.equatorial_moi;
1449 md.solidearth.rotational.polarmoi=structmd.slr.polar_moi;
1450 md.solidearth.rotational.angularvelocity=structmd.slr.angular_velocity;
1451 end
1452 end% }}}
1453 function md = tetras(md,varargin) % {{{
1454 %TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1455 %
1456 % Usage:
1457 % md=tetra(md)
1458
1459 if ~isa(md.mesh,'mesh3dprisms')
1460 error('mesh is not a 3d prismatic mesh');
1461 end
1462
1463 %Initialize tetra mesh
1464 md.mesh=mesh3dtetras(md.mesh);
1465
1466 %Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
1467 steiner = 0;
1468 nbv = md.mesh.numberofvertices;
1469 nbt = 3*md.mesh.numberofelements;
1470 elements = zeros(nbt,4);
1471 for i=1:md.mesh.numberofelements
1472 v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
1473 v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
1474 if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1475 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1476 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1477 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1478 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1479 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1480 elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
1481 elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
1482 elements(end+1,:) = [v2 v3 v5 v7];
1483 elements(end+1,:) = [v3 v5 v6 v7];
1484 elements(end+1,:) = [v1 v3 v6 v7];
1485 elements(end+1,:) = [v1 v4 v6 v7];
1486 elements(end+1,:) = [v4 v5 v6 v7];
1487 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1488 elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
1489 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1490 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1491 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1492 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1493 elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
1494 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1495 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1496 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1497 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1498 elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
1499 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1500 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1501 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1502 elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
1503 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1504 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1505 elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
1506 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1507 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1508 elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
1509 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1510 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1511 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1512 elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
1513 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1514 elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
1515 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1516 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1517 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1518 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1519 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1520 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1521 elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
1522 elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
1523 elements(end+1,:) = [v2 v5 v6 v7];
1524 elements(end+1,:) = [v2 v3 v6 v7];
1525 elements(end+1,:) = [v3 v4 v6 v7];
1526 elements(end+1,:) = [v1 v3 v4 v7];
1527 elements(end+1,:) = [v4 v5 v6 v7];
1528 else
1529 error('Case not supported'); %not supposed to happen!
1530 end
1531 %Reorder elements to make sure they are direct
1532 for j=1:3
1533 element = elements(3*(i-1)+j,:);
1534 matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
1535 if det(matrix)>0,
1536 elements(3*(i-1)+j,1)=element(2);
1537 elements(3*(i-1)+j,2)=element(1);
1538 end
1539 end
1540 end
1541 %%Split in 3 tetras
1542 %subelement1 = [1 2 3 5];
1543 %subelement2 = [4 6 5 1];
1544 %subelement3 = [5 6 3 1];
1545 %elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
1546 if steiner==0,
1547 disp('No Steiner point required to split prismatic mesh into tets');
1548 else
1549 disp([num2str(steiner) ' Steiner points had to be included'])
1550 error('Steiner point not supported yet');
1551 end
1552
1553 pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1554
1555 md.mesh.elements=elements;
1556 md.mesh.numberofelements=size(elements,1);
1557
1558 %p and q (same deal, except for element that are on the bedrock: )
1559 if ~isnan(md.friction.p),
1560 md.friction.p=md.friction.p(pos_elements);
1561 md.friction.q=md.friction.q(pos_elements);
1562 end
1563
1564 %elementstype
1565 if ~isnan(md.flowequation.element_equation)
1566 oldelements_type=md.flowequation.element_equation;
1567 md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1568 end
1569
1570 %connectivity
1571 md.mesh.elementconnectivity=NaN;
1572
1573 %materials
1574 if ~isnan(md.materials.rheology_n),
1575 md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1576 end
1577
1578 %increase connectivity if less than 25:
1579 if md.mesh.average_vertex_connectivity<=25,
1580 md.mesh.average_vertex_connectivity=100;
1581 end
1582 end % }}}
1583 function disp(self) % {{{
1584 disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
1585 disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
1586 disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1587 disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
1588 disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
1589 disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
1590 disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
1591 disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
1592 disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
1593 disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
1594 disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
1595 disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
1596 disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
1597 disp(sprintf('%19s: %-22s -- %s','solidearth' ,['[1x1 ' class(self.solidearth) ']'],'solidearth inputs and settings'));
1598 disp(sprintf('%19s: %-22s -- %s','dsl' ,['[1x1 ' class(self.dsl) ']'],'dynamic sea-level '));
1599 disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
1600 disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
1601 disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
1602 disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
1603 disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of CPUs...)'));
1604 disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
1605 disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
1606 disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
1607 disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
1608 disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
1609 disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
1610 disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
1611 disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parHwoameters for transient solution'));
1612 disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
1613 disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
1614 disp(sprintf('%19s: %-22s -- %s','frontalforcings' ,['[1x1 ' class(self.frontalforcings) ']'],'parameters for frontalforcings'));
1615 disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
1616 disp(sprintf('%19s: %-22s -- %s','love' ,['[1x1 ' class(self.love) ']'],'parameters for love solution'));
1617 disp(sprintf('%19s: %-22s -- %s','sampling' ,['[1x1 ' class(self.sampling) ']'],'parameters for stochastic sampler'));
1618 disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
1619 disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
1620 disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'Dakota properties'));
1621 disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
1622 disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
1623 disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
1624 disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
1625 disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
1626 end % }}}
1627 function memory(self) % {{{
1628
1629 disp(sprintf('\nMemory imprint:\n'));
1630
1631 fields=properties('model');
1632 mem=0;
1633
1634 for i=1:length(fields),
1635 field=self.(fields{i});
1636 s=whos('field');
1637 mem=mem+s.bytes/1e6;
1638 disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1639 end
1640 disp(sprintf('%19s--%10s','--------------','--------------'));
1641 disp(sprintf('%19s: %g Mb','Total',mem));
1642 end % }}}
1643 function netcdf(self,filename) % {{{
1644 %NETCDF - save model as netcdf
1645 %
1646 % Usage:
1647 % netcdf(md,filename)
1648 %
1649 % Example:
1650 % netcdf(md,'model.nc');
1651
1652 disp('Saving model as NetCDF');
1653 %1. Create NetCDF file
1654 ncid=netcdf.create(filename,'CLOBBER');
1655 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1656 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
1657 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1658 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1659
1660 %Preallocate variable id, needed to write variables in netcdf file
1661 var_id=zeros(1000,1);%preallocate
1662
1663 for step=1:2,
1664 counter=0;
1665 [var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
1666 if step==1, netcdf.endDef(ncid); end
1667 end
1668
1669 if counter>1000,
1670 warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1671 end
1672
1673 netcdf.close(ncid)
1674 end % }}}
1675 function xylim(self) % {{{
1676
1677 xlim([min(self.mesh.x) max(self.mesh.x)]);
1678 ylim([min(self.mesh.y) max(self.mesh.y)])
1679 end % }}}
1680 function md=upload(md) % {{{
1681 %the goal of this routine is to upload the model onto a server, and to empty it.
1682 %So first, save the model with a unique name and upload the file to the server:
1683 random_part=fix(rand(1)*10000);
1684 id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1685 eval(['save ' id ' md']);
1686
1687 %Now, upload the file:
1688 issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1689
1690 %Now, empty this model of everything except settings, and record name of file we just uploaded!
1691 settings_back=md.settings;
1692 md=model();
1693 md.settings=settings_back;
1694 md.settings.upload_filename=id;
1695
1696 %get locally rid of file that was uploaded
1697 eval(['delete ' id]);
1698
1699 end % }}}
1700 function md=download(md) % {{{
1701
1702 %the goal of this routine is to download the internals of the current model from a server, because
1703 %this model is empty, except for the settings which tell us where to go and find this model!
1704
1705 %Download the file:
1706 issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1707
1708 name=md.settings.upload_filename;
1709
1710 %Now, load this model:
1711 md=loadmodel(md.settings.upload_filename);
1712
1713 %get locally rid of file that was downloaded
1714 eval(['delete ' name]);
1715
1716 end % }}}
1717 function savemodeljs(md,modelname,websiteroot,varargin) % {{{
1718
1719 %the goal of this routine is to save the model as a javascript array that can be included in any html
1720 %file:
1721
1722 options=pairoptions(varargin{:});
1723 optimization=getfieldvalue(options,'optimize',0);
1724
1725
1726 %disp:
1727 disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
1728
1729 %open file for writing and declare the model:
1730 fid=fopen([websiteroot '/js/' modelname '.js'],'w');
1731 fprintf(fid,'var %s=new model();\n',modelname);
1732
1733 %now go through all the classes and fwrite all the corresponding fields:
1734
1735 fields=properties('model');
1736 for i=1:length(fields),
1737 field=fields{i};
1738
1739 %Some properties do not need to be saved
1740 if ismember(field,{'results','cluster' }),
1741 continue;
1742 end
1743
1744 %some optimization:
1745 if optimization==1,
1746 %optimize for plotting only:
1747 if ~ismember(field,{'geometry','mesh','mask'}),
1748 continue;
1749 end
1750 end
1751
1752 %Check that current field is an object
1753 if ~isobject(md.(field))
1754 error(['field ''' char(field) ''' is not an object']);
1755 end
1756
1757 %savemodeljs for current object
1758 %disp(['javascript saving ' field '...']);
1759 savemodeljs(md.(field),fid,modelname);
1760 end
1761
1762 %done, close file:
1763 fclose(fid);
1764 end
1765 end
1766 end
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