source: issm/trunk-jpl/src/m/classes/model.m@ 25119

Last change on this file since 25119 was 25119, checked in by Eric.Larour, 5 years ago

CHG: loading old models with slr in them.
File size: 72.1 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 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 end
205 %}}}
206 function md = checkmessage(md,string) % {{{
207 if(nargout~=1) error('wrong usage, model must be an output'); end
208 disp(['model not consistent: ' string]);
209 md.private.isconsistent=false;
210 end
211 %}}}
212 function md = collapse(md)% {{{
213 %COLLAPSE - collapses a 3d mesh into a 2d mesh
214 %
215 % This routine collapses a 3d model into a 2d model
216 % and collapses all the fileds of the 3d model by
217 % taking their depth-averaged values
218 %
219 % Usage:
220 % md=collapse(md)
221 %
222 % See also: EXTRUDE, MODELEXTRACT
223
224 %Check that the model is really a 3d model
225 if ~strcmp(md.mesh.elementtype(),'Penta'),
226 error('collapse error message: only 3d mesh can be collapsed')
227 end
228
229 %Start with changing all the fields from the 3d mesh
230
231 %dealing with the friction law
232 %drag is limited to nodes that are on the bedrock.
233 if isa(md.friction,'friction'),
234 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
235 md.friction.p=project2d(md,md.friction.p,1);
236 md.friction.q=project2d(md,md.friction.q,1);
237 elseif isa(md.friction,'frictioncoulomb'),
238 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
239 md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1);
240 md.friction.p=project2d(md,md.friction.p,1);
241 md.friction.q=project2d(md,md.friction.q,1);
242 elseif isa(md.friction,'frictionhydro'),
243 md.friction.q=project2d(md,md.friction.q,1);
244 md.friction.C=project2d(md,md.friction.C,1);
245 md.friction.As=project2d(md,md.friction.As,1);
246 md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
247 elseif isa(md.friction,'frictionwaterlayer'),
248 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
249 md.friction.p=project2d(md,md.friction.p,1);
250 md.friction.q=project2d(md,md.friction.q,1);
251 md.friction.water_layer=project2d(md,md.friction.water_layer,1);
252 elseif isa(md.friction,'frictionweertman'),
253 md.friction.C=project2d(md,md.friction.C,1);
254 md.friction.m=project2d(md,md.friction.m,1);
255 elseif isa(md.friction,'frictionweertmantemp'),
256 md.friction.C=project2d(md,md.friction.C,1);
257 md.friction.m=project2d(md,md.friction.m,1);
258 else
259 disp('friction type not supported');
260 end
261
262 %observations
263 if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
264 if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
265 if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
266 if ~isnan(md.inversion.thickness_obs), md.inversion.thickness_obs=project2d(md,md.inversion.thickness_obs,md.mesh.numberoflayers); end;
267 if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
268 if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
269 if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
270 if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
271 md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
272 elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
273 md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
274 end;
275
276 %results
277 if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
278 if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
279 if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
280 if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
281 if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
282 if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
283 if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
284 if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
285 if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
286 if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
287 if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
288 %giaivins
289 if isa(md.gia,'giaivins'),
290 if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
291 if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
292 end
293
294 %elementstype
295 if ~isnan(md.flowequation.element_equation)
296 md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
297 md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
298 md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
299 md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
300 md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
301 end
302
303 %boundary conditions
304 md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
305 md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
306 md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
307 md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
308 md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
309 if numel(md.masstransport.spcthickness)>1 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers); end
310 if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
311 if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
312 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
313
314 % Hydrologydc variables
315 if isa(md.hydrology,'hydrologydc');
316 md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
317 md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
318 md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
319 md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
320 if(md.hydrology.isefficientlayer==1)
321 md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
322 end
323 end
324
325 %materials
326 md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
327 md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
328
329 %damage:
330 if md.damage.isdamage,
331 md.damage.D=DepthAverage(md,md.damage.D);
332 end
333
334 %special for thermal modeling:
335 if ~isnan(md.basalforcings.groundedice_melting_rate),
336 md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
337 end
338 if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
339 md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
340 end
341 md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
342
343 if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
344 md.calving.coeff=project2d(md,md.calving.coeff,1);
345 end
346 if isprop(md.frontalforcings,'meltingrate') & ~isnan(md.frontalforcings.meltingrate),
347 md.frontalforcings.meltingrate=project2d(md,md.frontalforcings.meltingrate,1);
348 end
349
350 %update of connectivity matrix
351 md.mesh.average_vertex_connectivity=25;
352
353 %Collapse the mesh
354 nodes2d=md.mesh.numberofvertices2d;
355 elements2d=md.mesh.numberofelements2d;
356
357 %parameters
358 md.geometry.surface=project2d(md,md.geometry.surface,1);
359 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
360 md.geometry.base=project2d(md,md.geometry.base,1);
361 if ~isnan(md.geometry.bed),
362 md.geometry.bed=project2d(md,md.geometry.bed,1);
363 end
364
365 if ~isnan(md.mask.ocean_levelset),
366 md.mask.ocean_levelset=project2d(md,md.mask.ocean_levelset,1);
367 end
368 if ~isnan(md.mask.ice_levelset),
369 md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
370 end
371
372 %lat long
373 if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
374 if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
375
376 %outputdefinitions
377 for i=1:length(md.outputdefinition.definitions)
378 if isobject(md.outputdefinition.definitions{i})
379 %get subfields
380 solutionsubfields=fields(md.outputdefinition.definitions{i});
381 for j=1:length(solutionsubfields),
382 field=md.outputdefinition.definitions{i}.(solutionsubfields{j});
383 if length(field)==md.mesh.numberofvertices | length(field)==md.mesh.numberofelements,
384 md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1);
385 end
386 end
387 end
388 end
389
390 %Initialize with the 2d mesh
391 mesh=mesh2d();
392 mesh.x=md.mesh.x2d;
393 mesh.y=md.mesh.y2d;
394 mesh.numberofvertices=md.mesh.numberofvertices2d;
395 mesh.numberofelements=md.mesh.numberofelements2d;
396 mesh.elements=md.mesh.elements2d;
397 if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end
398 if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end
399 mesh.epsg=md.mesh.epsg;
400 if numel(md.mesh.scale_factor)==md.mesh.numberofvertices, mesh.scale_factor=project2d(md,md.mesh.scale_factor,1); end
401 if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
402 if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
403 md.mesh=mesh;
404 md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
405 md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
406 md.mesh.segments=contourenvelope(md.mesh);
407
408 end % }}}
409 function md2 = extract(md,area,varargin) % {{{
410 %extract - extract a model according to an Argus contour or flag list
411 %
412 % This routine extracts a submodel from a bigger model with respect to a given contour
413 % md must be followed by the corresponding exp file or flags list
414 % It can either be a domain file (argus type, .exp extension), or an array of element flags.
415 % If user wants every element outside the domain to be
416 % extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
417 % an empty string '' will be considered as an empty domain
418 % a string 'all' will be considered as the entire domain
419 %
420 % Usage:
421 % md2=extract(md,area);
422 %
423 % Examples:
424 % md2=extract(md,'Domain.exp');
425 %
426 % See also: EXTRUDE, COLLAPSE
427
428 %copy model
429 md1=md;
430
431 %recover optoins:
432 options=pairoptions(varargin{:});
433
434 %some checks
435 if ((nargin<2) | (nargout~=1)),
436 help extract
437 error('extract error message: bad usage');
438 end
439
440 %get elements that are inside area
441 flag_elem=FlagElements(md1,area);
442 if ~any(flag_elem),
443 error('extracted model is empty');
444 end
445
446 %kick out all elements with 3 dirichlets
447 if getfieldvalue(options,'spccheck',1)
448 spc_elem=find(~flag_elem);
449 spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
450 flag=ones(md1.mesh.numberofvertices,1);
451 flag(spc_node)=0;
452 pos=find(sum(flag(md1.mesh.elements),2)==0);
453 flag_elem(pos)=0;
454 end
455
456 %extracted elements and nodes lists
457 pos_elem=find(flag_elem);
458 pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
459
460 %keep track of some fields
461 numberofvertices1=md1.mesh.numberofvertices;
462 numberofelements1=md1.mesh.numberofelements;
463 numberofvertices2=length(pos_node);
464 numberofelements2=length(pos_elem);
465 flag_node=zeros(numberofvertices1,1);
466 flag_node(pos_node)=1;
467
468 %Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
469 Pelem=zeros(numberofelements1,1);
470 Pelem(pos_elem)=[1:numberofelements2]';
471 Pnode=zeros(numberofvertices1,1);
472 Pnode(pos_node)=[1:numberofvertices2]';
473
474 %renumber the elements (some nodes won't exist anymore)
475 elements_1=md1.mesh.elements;
476 elements_2=elements_1(pos_elem,:);
477 elements_2(:,1)=Pnode(elements_2(:,1));
478 elements_2(:,2)=Pnode(elements_2(:,2));
479 elements_2(:,3)=Pnode(elements_2(:,3));
480 if isa(md1.mesh,'mesh3dprisms'),
481 elements_2(:,4)=Pnode(elements_2(:,4));
482 elements_2(:,5)=Pnode(elements_2(:,5));
483 elements_2(:,6)=Pnode(elements_2(:,6));
484 end
485
486 %OK, now create the new model!
487
488 %take every field from model
489 md2=md1;
490
491 %automatically modify fields
492
493 %loop over model fields
494 model_fields=fields(md1);
495 for i=1:length(model_fields),
496 %get field
497 field=md1.(model_fields{i});
498 fieldsize=size(field);
499 if isobject(field), %recursive call
500 object_fields=fields(md1.(model_fields{i}));
501 for j=1:length(object_fields),
502 %get field
503 field=md1.(model_fields{i}).(object_fields{j});
504 fieldsize=size(field);
505 %size = number of nodes * n
506 if fieldsize(1)==numberofvertices1
507 md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
508 elseif (fieldsize(1)==numberofvertices1+1)
509 md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
510 %size = number of elements * n
511 elseif fieldsize(1)==numberofelements1
512 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
513 elseif (fieldsize(1)==numberofelements1+1)
514 md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
515 end
516 end
517 else
518 %size = number of nodes * n
519 if fieldsize(1)==numberofvertices1
520 md2.(model_fields{i})=field(pos_node,:);
521 elseif (fieldsize(1)==numberofvertices1+1)
522 md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
523 %size = number of elements * n
524 elseif fieldsize(1)==numberofelements1
525 md2.(model_fields{i})=field(pos_elem,:);
526 elseif (fieldsize(1)==numberofelements1+1)
527 md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
528 end
529 end
530 end
531
532 %modify some specific fields
533
534 %Mesh
535 md2.mesh.numberofelements=numberofelements2;
536 md2.mesh.numberofvertices=numberofvertices2;
537 md2.mesh.elements=elements_2;
538
539 %mesh.uppervertex mesh.lowervertex
540 if isa(md1.mesh,'mesh3dprisms'),
541 md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
542 pos=find(~isnan(md2.mesh.uppervertex));
543 md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
544
545 md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
546 pos=find(~isnan(md2.mesh.lowervertex));
547 md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
548
549 md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
550 pos=find(~isnan(md2.mesh.upperelements));
551 md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
552
553 md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
554 pos=find(~isnan(md2.mesh.lowerelements));
555 md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
556 end
557
558 %Initial 2d mesh
559 if isa(md1.mesh,'mesh3dprisms'),
560 flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
561 pos_elem_2d=find(flag_elem_2d);
562 flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
563 pos_node_2d=find(flag_node_2d);
564
565 md2.mesh.numberofelements2d=length(pos_elem_2d);
566 md2.mesh.numberofvertices2d=length(pos_node_2d);
567 md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
568 md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
569 md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
570 md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
571
572 md2.mesh.x2d=md1.mesh.x(pos_node_2d);
573 md2.mesh.y2d=md1.mesh.y(pos_node_2d);
574 end
575
576 %Edges
577 if(dimension(md.mesh)==2),
578 if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
579 %renumber first two columns
580 pos=find(md2.mesh.edges(:,4)~=-1);
581 md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
582 md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
583 md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
584 md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
585 %remove edges when the 2 vertices are not in the domain.
586 md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
587 %Replace all zeros by -1 in the last two columns
588 pos=find(md2.mesh.edges(:,3)==0);
589 md2.mesh.edges(pos,3)=-1;
590 pos=find(md2.mesh.edges(:,4)==0);
591 md2.mesh.edges(pos,4)=-1;
592 %Invert -1 on the third column with last column (Also invert first two columns!!)
593 pos=find(md2.mesh.edges(:,3)==-1);
594 md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
595 md2.mesh.edges(pos,4)=-1;
596 values=md2.mesh.edges(pos,2);
597 md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
598 md2.mesh.edges(pos,1)=values;
599 %Finally remove edges that do not belong to any element
600 pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
601 md2.mesh.edges(pos,:)=[];
602 end
603 end
604
605 %Penalties
606 if ~isnan(md2.stressbalance.vertex_pairing),
607 for i=1:size(md1.stressbalance.vertex_pairing,1);
608 md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
609 end
610 md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
611 end
612 if ~isnan(md2.masstransport.vertex_pairing),
613 for i=1:size(md1.masstransport.vertex_pairing,1);
614 md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
615 end
616 md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
617 end
618
619 %recreate segments
620 if isa(md1.mesh,'mesh2d') | isa(md1.mesh','mesh3dsurface'),
621 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
622 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
623 md2.mesh.segments=contourenvelope(md2.mesh);
624 md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
625 else
626 %First do the connectivity for the contourenvelope in 2d
627 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
628 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
629 segments=contourenvelope(md2.mesh);
630 md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
631 md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
632 %Then do it for 3d as usual
633 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
634 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
635 end
636
637 %Boundary conditions: Dirichlets on new boundary
638 %Catch the elements that have not been extracted
639 orphans_elem=find(~flag_elem);
640 orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
641 %Figure out which node are on the boundary between md2 and md1
642 nodestoflag1=intersect(orphans_node,pos_node);
643 nodestoflag2=Pnode(nodestoflag1);
644 if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>1 & numel(md1.stressbalance.spcvz)>1,
645 if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
646 md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
647 md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
648 else
649 md2.stressbalance.spcvx(nodestoflag2)=NaN;
650 md2.stressbalance.spcvy(nodestoflag2)=NaN;
651 disp(' ')
652 disp('!! extract warning: spc values should be checked !!')
653 disp(' ')
654 end
655 %put 0 for vz
656 md2.stressbalance.spcvz(nodestoflag2)=0;
657 end
658 if ~isnan(md1.thermal.spctemperature),
659 md2.thermal.spctemperature(nodestoflag2,1)=1;
660 end
661
662 %Results fields
663 if isstruct(md1.results),
664 md2.results=struct();
665 solutionfields=fields(md1.results);
666 for i=1:length(solutionfields),
667 if isstruct(md1.results.(solutionfields{i}))
668 %get subfields
669 % loop over time steps
670 for p=1:length(md1.results.(solutionfields{i}))
671 current = md1.results.(solutionfields{i})(p);
672 solutionsubfields=fields(current);
673 for j=1:length(solutionsubfields),
674 field=md1.results.(solutionfields{i})(p).(solutionsubfields{j});
675 if length(field)==numberofvertices1,
676 md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_node);
677 elseif length(field)==numberofelements1,
678 md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_elem);
679 else
680 md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field;
681 end
682 end
683 end
684 else
685 field=md1.results.(solutionfields{i});
686 if length(field)==numberofvertices1,
687 md2.results.(solutionfields{i})=field(pos_node);
688 elseif length(field)==numberofelements1,
689 md2.results.(solutionfields{i})=field(pos_elem);
690 else
691 md2.results.(solutionfields{i})=field;
692 end
693 end
694 end
695 end
696
697 %OutputDefinitions fields
698 for i=1:length(md1.outputdefinition.definitions),
699 if isobject(md1.outputdefinition.definitions{i})
700 %get subfields
701 solutionsubfields=fields(md1.outputdefinition.definitions{i});
702 for j=1:length(solutionsubfields),
703 field=md1.outputdefinition.definitions{i}.(solutionsubfields{j});
704 if length(field)==numberofvertices1,
705 md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node);
706 elseif length(field)==numberofelements1,
707 md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem);
708 end
709 end
710 end
711 end
712
713 %Keep track of pos_node and pos_elem
714 md2.mesh.extractedvertices=pos_node;
715 md2.mesh.extractedelements=pos_elem;
716 end % }}}
717 function md = extrude(md,varargin) % {{{
718 %EXTRUDE - vertically extrude a 2d mesh
719 %
720 % vertically extrude a 2d mesh and create corresponding 3d mesh.
721 % The vertical distribution can:
722 % - follow a polynomial law
723 % - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
724 % - be discribed by a list of coefficients (between 0 and 1)
725 %
726 %
727 % Usage:
728 % md=extrude(md,numlayers,extrusionexponent);
729 % md=extrude(md,numlayers,lowerexponent,upperexponent);
730 % md=extrude(md,listofcoefficients);
731 %
732 % Example:
733 % md=extrude(md,15,1.3);
734 % md=extrude(md,15,1.3,1.2);
735 % md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
736 %
737 % See also: MODELEXTRACT, COLLAPSE
738
739 %some checks on list of arguments
740 if ((nargin>4) | (nargin<2) | (nargout~=1)),
741 help extrude;
742 error('extrude error message');
743 end
744 if numel(md.geometry.base)~=md.mesh.numberofvertices || numel(md.geometry.surface)~=md.mesh.numberofvertices
745 error('model has not been parameterized yet: base and/or surface not set');
746 end
747
748 %Extrude the mesh
749 if nargin==2, %list of coefficients
750 clist=varargin{1};
751 if any(clist<0) | any(clist>1),
752 error('extrusioncoefficients must be between 0 and 1');
753 end
754 extrusionlist=sort(unique([clist(:);0;1]));
755 numlayers=length(extrusionlist);
756 elseif nargin==3, %one polynomial law
757 if varargin{2}<=0,
758 help extrude;
759 error('extrusionexponent must be >=0');
760 end
761 numlayers=varargin{1};
762 extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
763 elseif nargin==4, %two polynomial laws
764 numlayers=varargin{1};
765 lowerexp=varargin{2};
766 upperexp=varargin{3};
767
768 if varargin{2}<=0 | varargin{3}<=0,
769 help extrude;
770 error('lower and upper extrusionexponents must be >=0');
771 end
772
773 lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
774 upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
775 extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
776
777 end
778
779 if numlayers<2,
780 error('number of layers should be at least 2');
781 end
782 if strcmp(md.mesh.domaintype(),'3D')
783 error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
784 end
785
786 %Initialize with the 2d mesh
787 mesh2d = md.mesh;
788 md.mesh=mesh3dprisms();
789 md.mesh.x = mesh2d.x;
790 md.mesh.y = mesh2d.y;
791 md.mesh.elements = mesh2d.elements;
792 md.mesh.numberofelements = mesh2d.numberofelements;
793 md.mesh.numberofvertices = mesh2d.numberofvertices;
794
795 md.mesh.lat = mesh2d.lat;
796 md.mesh.long = mesh2d.long;
797 md.mesh.epsg = mesh2d.epsg;
798 md.mesh.scale_factor = mesh2d.scale_factor;
799
800 md.mesh.vertexonboundary = mesh2d.vertexonboundary;
801 md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
802 md.mesh.elementconnectivity = mesh2d.elementconnectivity;
803 md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
804
805 md.mesh.extractedvertices = mesh2d.extractedvertices;
806 md.mesh.extractedelements = mesh2d.extractedelements;
807
808 x3d=[];
809 y3d=[];
810 z3d=[]; %the lower node is on the bed
811 thickness3d=md.geometry.thickness; %thickness and bed for these nodes
812 bed3d=md.geometry.base;
813
814 %Create the new layers
815 for i=1:numlayers,
816 x3d=[x3d; md.mesh.x];
817 y3d=[y3d; md.mesh.y];
818 %nodes are distributed between bed and surface accordingly to the given exponent
819 z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
820 end
821 number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
822
823 %Extrude elements
824 elements3d=[];
825 for i=1:numlayers-1,
826 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
827 end
828 number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
829
830 %Keep a trace of lower and upper nodes
831 lowervertex=NaN*ones(number_nodes3d,1);
832 uppervertex=NaN*ones(number_nodes3d,1);
833 lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
834 uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
835 md.mesh.lowervertex=lowervertex;
836 md.mesh.uppervertex=uppervertex;
837
838 %same for lower and upper elements
839 lowerelements=NaN*ones(number_el3d,1);
840 upperelements=NaN*ones(number_el3d,1);
841 lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
842 upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
843 md.mesh.lowerelements=lowerelements;
844 md.mesh.upperelements=upperelements;
845
846 %Save old mesh
847 md.mesh.x2d=md.mesh.x;
848 md.mesh.y2d=md.mesh.y;
849 md.mesh.elements2d=md.mesh.elements;
850 md.mesh.numberofelements2d=md.mesh.numberofelements;
851 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
852
853 %Build global 3d mesh
854 md.mesh.elements=elements3d;
855 md.mesh.x=x3d;
856 md.mesh.y=y3d;
857 md.mesh.z=z3d;
858 md.mesh.numberofelements=number_el3d;
859 md.mesh.numberofvertices=number_nodes3d;
860 md.mesh.numberoflayers=numlayers;
861
862 %Ok, now deal with the other fields from the 2d mesh:
863
864 %bedinfo and surface info
865 md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
866 md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
867 md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
868
869 %lat long
870 md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
871 md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
872 md.mesh.scale_factor=project3d(md,'vector',md.mesh.scale_factor,'type','node');
873
874 md.geometry=extrude(md.geometry,md);
875 md.friction = extrude(md.friction,md);
876 md.inversion = extrude(md.inversion,md);
877 md.smb = extrude(md.smb,md);
878 md.initialization = extrude(md.initialization,md);
879
880 md.flowequation=md.flowequation.extrude(md);
881 md.stressbalance=extrude(md.stressbalance,md);
882 md.thermal=md.thermal.extrude(md);
883 md.masstransport=md.masstransport.extrude(md);
884 md.levelset=extrude(md.levelset,md);
885 md.calving=extrude(md.calving,md);
886 md.frontalforcings=extrude(md.frontalforcings,md);
887 md.hydrology = extrude(md.hydrology,md);
888 md.solidearth = extrude(md.solidearth,md);
889 md.dsl = extrude(md.dsl,md);
890
891 %connectivity
892 if ~isnan(md.mesh.elementconnectivity)
893 md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
894 md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
895 for i=2:numlayers-1,
896 md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
897 =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
898 end
899 md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
900 end
901
902 md.materials=extrude(md.materials,md);
903 md.damage=extrude(md.damage,md);
904 md.mask=extrude(md.mask,md);
905 md.qmu=extrude(md.qmu,md);
906 md.basalforcings=extrude(md.basalforcings,md);
907 md.outputdefinition=extrude(md.outputdefinition,md);
908
909 %increase connectivity if less than 25:
910 if md.mesh.average_vertex_connectivity<=25,
911 md.mesh.average_vertex_connectivity=100;
912 end
913 end % }}}
914 function md = structtomodel(md,structmd) % {{{
915
916 if ~isstruct(structmd) error('input model is not a structure'); end
917
918 %loaded model is a struct, initialize output and recover all fields
919 md = structtoobj(model,structmd);
920
921 %Old field now classes
922 if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
923 if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
924
925 %Field name change
926 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
927 if isfield(structmd,'p'), md.friction.p=structmd.p; end
928 if isfield(structmd,'q'), md.friction.q=structmd.p; end
929 if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
930 if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
931 if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
932 if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
933 if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
934 if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
935 if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
936 if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
937 if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
938 if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
939 if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
940 if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
941 if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
942 if isfield(structmd,'g'), md.constants.g=structmd.g; end
943 if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
944 if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
945 if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
946 if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
947 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
948 if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
949 if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
950 if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
951 if isfield(structmd,'riftproperties'), %old implementation
952 md.rifts=rifts();
953 md.rifts.riftproperties=structmd.riftproperties;
954 md.rifts.riftstruct=structmd.rifts;
955 md.rifts.riftproperties=structmd.riftinfo;
956 end
957 if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
958 if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
959 if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
960 if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
961 if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
962 if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
963 if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
964 if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
965 if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
966 if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
967 if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
968 if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
969 if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
970 if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
971 if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
972 if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
973 if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
974 if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
975 if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
976 if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
977 if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
978 if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
979 if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
980 if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
981 if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
982 if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
983 if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
984 if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
985 if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
986 if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
987 if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
988 if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
989 if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
990 if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
991 if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
992 if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
993 if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
994 if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
995 if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
996 if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
997 if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
998 if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
999 if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
1000 if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
1001 if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
1002 if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
1003 if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
1004 if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
1005 if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
1006 if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
1007 if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
1008 if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
1009 if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
1010 if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
1011 if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
1012 if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
1013 if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
1014 if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
1015 if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
1016 if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
1017 if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
1018 if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
1019 if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
1020 if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
1021 if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
1022 if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
1023 if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
1024 if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
1025 if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
1026 if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
1027 if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
1028 if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
1029 if isfield(structmd,'long'), md.mesh.long=structmd.long; end
1030 if isfield(structmd,'scale_factor'), md.mesh.scale_factor=structmd.scale_factor; end
1031 if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
1032 if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
1033 if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
1034 if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
1035 if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
1036 if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
1037 if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
1038 if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
1039 if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
1040 if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
1041 if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
1042 if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
1043 if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
1044 if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
1045 if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
1046 if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
1047 if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
1048 if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
1049 if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
1050 if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
1051 if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
1052 if isfield(structmd,'edges'),
1053 md.mesh.edges=structmd.edges;
1054 md.mesh.edges(isnan(md.mesh.edges))=-1;
1055 end
1056 if isfield(structmd,'y'), md.mesh.y=structmd.y; end
1057 if isfield(structmd,'x'), md.mesh.x=structmd.x; end
1058 if isfield(structmd,'z'), md.mesh.z=structmd.z; end
1059 if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
1060 if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
1061 if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
1062
1063 if isnumeric(md.verbose),
1064 md.verbose=verbose;
1065 end
1066
1067 if isfield(structmd,'spcvelocity'),
1068 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
1069 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
1070 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1071 pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
1072 pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
1073 pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
1074 end
1075 if isfield(structmd,'spcvx'),
1076 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
1077 pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
1078 end
1079 if isfield(structmd,'spcvy'),
1080 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
1081 pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
1082 end
1083 if isfield(structmd,'spcvz'),
1084 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1085 pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
1086 end
1087 if isfield(structmd,'pressureload'),
1088 if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
1089 pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
1090 pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
1091 pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
1092 end
1093 end
1094 if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
1095 pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
1096 pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
1097 pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
1098 pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
1099 pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
1100 pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
1101 pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
1102 pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
1103 end
1104 if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
1105 pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
1106 pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
1107 pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
1108 pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
1109 pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
1110 pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
1111 pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
1112 pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
1113 end
1114 if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
1115 if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
1116 if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1117 if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1118 end
1119 if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1120 if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1121 if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
1122 if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1123 end
1124 if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1125 if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1126 if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1127 if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1128 end
1129 if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1130 pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1131 pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1132 pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1133 pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1134 pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1135 pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1136 pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1137 pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1138 pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1139 end
1140
1141 if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1142 md.thermal.stabilization=2;
1143 md.masstransport.stabilization=1;
1144 md.balancethickness.stabilization=1;
1145 end
1146 if isnumeric(md.masstransport.hydrostatic_adjustment)
1147 if md.masstransport.hydrostatic_adjustment==269,
1148 md.masstransport.hydrostatic_adjustment='Incremental';
1149 else
1150 md.masstransport.hydrostatic_adjustment='Absolute';
1151 end
1152 end
1153
1154 %New fields
1155 if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
1156 md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1157 md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1158 end
1159 if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
1160 md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1161 md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1162 end
1163 if ~isfield(structmd,'diagnostic_ref');
1164 md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1165 end
1166 if ~isfield(structmd,'loadingforce');
1167 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1168 end
1169
1170 %2013 August 9
1171 if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1172 disp('Recovering old prognostic class');
1173 md.masstransport=masstransport(structmd.prognostic);
1174 end
1175 %2013 August 9
1176 if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') || isa(structmd.diagnostic,'stressbalance')),
1177 disp('Recovering old diagnostic class');
1178 md.stressbalance=stressbalance(structmd.diagnostic);
1179 end
1180 %2014 January 9th
1181 if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
1182 disp('Recovering old surfaceforcings class');
1183 mass_balance=structmd.surfaceforcings.mass_balance;
1184 md.smb=SMB();
1185 md.smb.mass_balance=mass_balance;
1186 end
1187 %2015 September 10
1188 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
1189 disp('Recovering old SMB class');
1190 md.smb=SMBforcing(structmd.surfaceforcings);
1191 end
1192 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
1193 disp('Recovering old SMBhenning class');
1194 md.smb=SMBhenning(structmd.surfaceforcings);
1195 end
1196 if isfield(structmd,'slr'),
1197 disp('Recovering old slr class');
1198 md.solidearth.sealevel=structmd.slr.sealevel;
1199 md.solidearth.planetradius=structmd.slr.planetradius;
1200 md.solidearth.requested_outputs=structmd.slr.requested_outputs;
1201 md.solidearth.transitions=structmd.slr.transitions;
1202
1203 md.solidearth.transitions=structmd.slr.transitions;
1204 md.solidearth.settings.reltol=structmd.slr.reltol;
1205 md.solidearth.settings.abstol=structmd.slr.abstol;
1206 md.solidearth.settings.maxiter=structmd.slr.maxiter;
1207 md.solidearth.settings.rigid=structmd.slr.rigid;
1208 md.solidearth.settings.elastic=structmd.slr.elastic;
1209 md.solidearth.settings.rotation=structmd.slr.rotation;
1210 md.solidearth.settings.runfrequency=structmd.slr.geodetic_run_frequency;
1211 md.solidearth.settings.computesealevelchange=structmd.slr.geodetic;
1212 md.solidearth.settings.degacc=structmd.slr.degacc;
1213 md.solidearth.settings.horiz=structmd.slr.horiz;
1214 md.solidearth.settings.ocean_area_scaling=structmd.slr.ocean_area_scaling;
1215
1216 md.solidearth.surfaceload.icethicknesschange=structmd.slr.deltathickness;
1217 md.solidearth.surfaceload.waterheightchange=structmd.slr.hydro_rate;
1218
1219 md.solidearth.love.h=structmd.slr.love_h;
1220 md.solidearth.love.k=structmd.slr.love_k;
1221 md.solidearth.love.l=structmd.slr.love_l;
1222 md.solidearth.love.th=structmd.slr.tide_love_h;
1223 md.solidearth.love.tk=structmd.slr.tide_love_k;
1224 md.solidearth.love.tk2secular=structmd.slr.fluid_love;
1225
1226 md.solidearth.rotational.equatorialmoi=structmd.slr.equatorial_moi;
1227 md.solidearth.rotational.polarmoi=structmd.slr.polar_moi;
1228 md.solidearth.rotational.angularvelocity=structmd.slr.angular_velocity;
1229 end
1230 end% }}}
1231 function md = setdefaultparameters(md) % {{{
1232
1233 %initialize subclasses
1234 md.mesh = mesh2d();
1235 md.mask = mask();
1236 md.constants = constants();
1237 md.geometry = geometry();
1238 md.initialization = initialization();
1239 md.smb = SMBforcing();
1240 md.basalforcings = basalforcings();
1241 md.friction = friction();
1242 md.rifts = rifts();
1243 md.solidearth = solidearth();
1244 md.dsl = dsl();
1245 md.timestepping = timestepping();
1246 md.groundingline = groundingline();
1247 md.materials = matice();
1248 md.damage = damage();
1249 md.flowequation = flowequation();
1250 md.debug = debug();
1251 md.verbose = verbose();
1252 md.settings = issmsettings();
1253 md.toolkits = toolkits();
1254 md.cluster = generic();
1255 md.balancethickness = balancethickness();
1256 md.stressbalance = stressbalance();
1257 md.hydrology = hydrologyshreve();
1258 md.masstransport = masstransport();
1259 md.thermal = thermal();
1260 md.steadystate = steadystate();
1261 md.transient = transient();
1262 md.levelset = levelset();
1263 md.calving = calving();
1264 md.frontalforcings = frontalforcings();
1265 md.gia = giamme();
1266 md.esa = esa();
1267 md.love = fourierlove();
1268 md.esa = esa();
1269 md.autodiff = autodiff();
1270 md.inversion = inversion();
1271 md.qmu = qmu();
1272 md.amr = amr();
1273 md.radaroverlay = radaroverlay();
1274 md.results = struct();
1275 md.outputdefinition = outputdefinition();
1276 md.miscellaneous = miscellaneous();
1277 md.private = private();
1278 end
1279 %}}}
1280 function md = tetras(md,varargin) % {{{
1281 %TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1282 %
1283 % Usage:
1284 % md=tetra(md)
1285
1286 if ~isa(md.mesh,'mesh3dprisms')
1287 error('mesh is not a 3d prismatic mesh');
1288 end
1289
1290 %Initialize tetra mesh
1291 md.mesh=mesh3dtetras(md.mesh);
1292
1293 %Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
1294 steiner = 0;
1295 nbv = md.mesh.numberofvertices;
1296 nbt = 3*md.mesh.numberofelements;
1297 elements = zeros(nbt,4);
1298 for i=1:md.mesh.numberofelements
1299 v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
1300 v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
1301 if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1302 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1303 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1304 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1305 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1306 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1307 elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
1308 elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
1309 elements(end+1,:) = [v2 v3 v5 v7];
1310 elements(end+1,:) = [v3 v5 v6 v7];
1311 elements(end+1,:) = [v1 v3 v6 v7];
1312 elements(end+1,:) = [v1 v4 v6 v7];
1313 elements(end+1,:) = [v4 v5 v6 v7];
1314 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1315 elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
1316 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1317 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1318 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1319 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1320 elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
1321 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1322 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1323 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1324 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1325 elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
1326 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1327 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1328 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1329 elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
1330 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1331 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1332 elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
1333 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1334 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1335 elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
1336 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1337 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1338 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1339 elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
1340 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1341 elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
1342 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1343 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1344 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1345 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1346 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1347 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1348 elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
1349 elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
1350 elements(end+1,:) = [v2 v5 v6 v7];
1351 elements(end+1,:) = [v2 v3 v6 v7];
1352 elements(end+1,:) = [v3 v4 v6 v7];
1353 elements(end+1,:) = [v1 v3 v4 v7];
1354 elements(end+1,:) = [v4 v5 v6 v7];
1355 else
1356 error('Case not supported'); %not supposed to happen!
1357 end
1358 %Reorder elements to make sure they are direct
1359 for j=1:3
1360 element = elements(3*(i-1)+j,:);
1361 matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
1362 if det(matrix)>0,
1363 elements(3*(i-1)+j,1)=element(2);
1364 elements(3*(i-1)+j,2)=element(1);
1365 end
1366 end
1367 end
1368 %%Split in 3 tetras
1369 %subelement1 = [1 2 3 5];
1370 %subelement2 = [4 6 5 1];
1371 %subelement3 = [5 6 3 1];
1372 %elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
1373 if steiner==0,
1374 disp('No Steiner point required to split prismatic mesh into tets');
1375 else
1376 disp([num2str(steiner) ' Steiner points had to be included'])
1377 error('Steiner point not supported yet');
1378 end
1379
1380 pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1381
1382 md.mesh.elements=elements;
1383 md.mesh.numberofelements=size(elements,1);
1384
1385 %p and q (same deal, except for element that are on the bedrock: )
1386 if ~isnan(md.friction.p),
1387 md.friction.p=md.friction.p(pos_elements);
1388 md.friction.q=md.friction.q(pos_elements);
1389 end
1390
1391 %elementstype
1392 if ~isnan(md.flowequation.element_equation)
1393 oldelements_type=md.flowequation.element_equation;
1394 md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1395 end
1396
1397 %connectivity
1398 md.mesh.elementconnectivity=NaN;
1399
1400 %materials
1401 if ~isnan(md.materials.rheology_n),
1402 md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1403 end
1404
1405 %increase connectivity if less than 25:
1406 if md.mesh.average_vertex_connectivity<=25,
1407 md.mesh.average_vertex_connectivity=100;
1408 end
1409 end % }}}
1410 function disp(self) % {{{
1411 disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
1412 disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
1413 disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1414 disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
1415 disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
1416 disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
1417 disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
1418 disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
1419 disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
1420 disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
1421 disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
1422 disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
1423 disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
1424 disp(sprintf('%19s: %-22s -- %s','solidearth' ,['[1x1 ' class(self.solidearth) ']'],'solidearth inputs and settings'));
1425 disp(sprintf('%19s: %-22s -- %s','dsl' ,['[1x1 ' class(self.dsl) ']'],'dynamic sea-level '));
1426 disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
1427 disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
1428 disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
1429 disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
1430 disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
1431 disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
1432 disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
1433 disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
1434 disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
1435 disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
1436 disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
1437 disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
1438 disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
1439 disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
1440 disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
1441 disp(sprintf('%19s: %-22s -- %s','frontalforcings' ,['[1x1 ' class(self.frontalforcings) ']'],'parameters for frontalforcings'));
1442 disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
1443 disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
1444 disp(sprintf('%19s: %-22s -- %s','love' ,['[1x1 ' class(self.love) ']'],'parameters for love solution'));
1445 disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
1446 disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
1447 disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
1448 disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
1449 disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
1450 disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
1451 disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
1452 disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
1453 end % }}}
1454 function memory(self) % {{{
1455
1456 disp(sprintf('\nMemory imprint:\n'));
1457
1458 fields=properties('model');
1459 mem=0;
1460
1461 for i=1:length(fields),
1462 field=self.(fields{i});
1463 s=whos('field');
1464 mem=mem+s.bytes/1e6;
1465 disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1466 end
1467 disp(sprintf('%19s--%10s','--------------','--------------'));
1468 disp(sprintf('%19s: %g Mb','Total',mem));
1469 end % }}}
1470 function netcdf(self,filename) % {{{
1471 %NETCDF - save model as netcdf
1472 %
1473 % Usage:
1474 % netcdf(md,filename)
1475 %
1476 % Example:
1477 % netcdf(md,'model.nc');
1478
1479 disp('Saving model as NetCDF');
1480 %1. Create NetCDF file
1481 ncid=netcdf.create(filename,'CLOBBER');
1482 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1483 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
1484 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1485 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1486
1487 %Preallocate variable id, needed to write variables in netcdf file
1488 var_id=zeros(1000,1);%preallocate
1489
1490 for step=1:2,
1491 counter=0;
1492 [var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
1493 if step==1, netcdf.endDef(ncid); end
1494 end
1495
1496 if counter>1000,
1497 warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1498 end
1499
1500 netcdf.close(ncid)
1501 end % }}}
1502 function xylim(self) % {{{
1503
1504 xlim([min(self.mesh.x) max(self.mesh.x)]);
1505 ylim([min(self.mesh.y) max(self.mesh.y)])
1506 end % }}}
1507 function md=upload(md) % {{{
1508 %the goal of this routine is to upload the model onto a server, and to empty it.
1509 %So first, save the model with a unique name and upload the file to the server:
1510 random_part=fix(rand(1)*10000);
1511 id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1512 eval(['save ' id ' md']);
1513
1514 %Now, upload the file:
1515 issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1516
1517 %Now, empty this model of everything except settings, and record name of file we just uploaded!
1518 settings_back=md.settings;
1519 md=model();
1520 md.settings=settings_back;
1521 md.settings.upload_filename=id;
1522
1523 %get locally rid of file that was uploaded
1524 eval(['delete ' id]);
1525
1526 end % }}}
1527 function md=download(md) % {{{
1528
1529 %the goal of this routine is to download the internals of the current model from a server, because
1530 %this model is empty, except for the settings which tell us where to go and find this model!
1531
1532 %Download the file:
1533 issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1534
1535 name=md.settings.upload_filename;
1536
1537 %Now, load this model:
1538 md=loadmodel(md.settings.upload_filename);
1539
1540 %get locally rid of file that was downloaded
1541 eval(['delete ' name]);
1542
1543 end % }}}
1544 function savemodeljs(md,modelname,websiteroot,varargin) % {{{
1545
1546 %the goal of this routine is to save the model as a javascript array that can be included in any html
1547 %file:
1548
1549 options=pairoptions(varargin{:});
1550 optimization=getfieldvalue(options,'optimize',0);
1551
1552
1553 %disp:
1554 disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
1555
1556 %open file for writing and declare the model:
1557 fid=fopen([websiteroot '/js/' modelname '.js'],'w');
1558 fprintf(fid,'var %s=new model();\n',modelname);
1559
1560 %now go through all the classes and fwrite all the corresponding fields:
1561
1562 fields=properties('model');
1563 for i=1:length(fields),
1564 field=fields{i};
1565
1566 %Some properties do not need to be saved
1567 if ismember(field,{'results','cluster' }),
1568 continue;
1569 end
1570
1571 %some optimization:
1572 if optimization==1,
1573 %optimize for plotting only:
1574 if ~ismember(field,{'geometry','mesh','mask'}),
1575 continue;
1576 end
1577 end
1578
1579 %Check that current field is an object
1580 if ~isobject(md.(field))
1581 error(['field ''' char(field) ''' is not an object']);
1582 end
1583
1584 %savemodeljs for current object
1585 %disp(['javascript saving ' field '...']);
1586 savemodeljs(md.(field),fid,modelname);
1587 end
1588
1589 %done, close file:
1590 fclose(fid);
1591 end
1592 end
1593 end
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