source: issm/trunk-jpl/src/m/classes/model.m@ 25758

Last change on this file since 25758 was 25758, checked in by jdquinn, 4 years ago

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