source: issm/trunk-jpl/src/m/classes/model.m@ 23434

Last change on this file since 23434 was 23434, checked in by tsantos, 6 years ago

BUG: check md.settings before define new value for solver_residue_threshold
File size: 68.3 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 slr = 0;
25
26 debug = 0;
27 verbose = 0;
28 settings = 0;
29 toolkits = 0;
30 cluster = 0;
31
32 balancethickness = 0;
33 stressbalance = 0;
34 groundingline = 0;
35 hydrology = 0;
36 masstransport = 0;
37 thermal = 0;
38 steadystate = 0;
39 transient = 0;
40 levelset = 0;
41 calving = 0;
42 love = 0;
43 gia = 0;
44 esa = 0;
45
46 autodiff = 0;
47 inversion = 0;
48 qmu = 0;
49 amr = 0;
50 results = 0;
51 outputdefinition = 0;
52 radaroverlay = 0;
53 miscellaneous = 0;
54 private = 0;
55
56 %}}}
57 end
58 methods (Static)
59 function md = loadobj(md) % {{{
60 % This function is directly called by matlab when a model object is
61 % loaded. If the input is a struct it is an old version of model and
62 % old fields must be recovered (make sure they are in the deprecated
63 % model properties)
64
65 if verLessThan('matlab','7.9'),
66 disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
67 disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
68
69 % This is a Matlab bug: all the fields of md have their default value
70 % Example of error message:
71 % Warning: Error loading an object of class 'model':
72 % Undefined function or method 'exist' for input arguments of type 'cell'
73 %
74 % This has been fixed in MATLAB 7.9 (R2009b) and later versions
75 end
76
77 if isstruct(md)
78 disp('Recovering model object from a previous version');
79 md = structtomodel(model,md);
80 end
81
82 %2012 August 4th
83 if isa(md.materials,'materials'),
84 disp('Recovering old materials');
85 if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
86 md.materials=matice(md.materials);
87 else
88 md.materials=matdamageice(md.materials);
89 end
90 end
91 %2013 April 12
92 if numel(md.stressbalance.loadingforce==1)
93 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
94 end
95 %2013 April 17
96 if isa(md.hydrology,'hydrology'),
97 disp('Recovering old hydrology class');
98 md.hydrology=hydrologyshreve(md.materials);
99 end
100 %2013 October 9
101 if ~isa(md.damage,'damage'),
102 md.damage=damage();
103 md.damage.D=zeros(md.mesh.numberofvertices,1);
104 md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
105 end
106 %2013 November 18
107 if ~isa(md.outputdefinition,'outputdefinition'),
108 md.outputdefinition=outputdefinition();
109 end
110 %2014 March 26th
111 if isa(md.mesh,'mesh'),
112 disp('Recovering old mesh class');
113 if isprop(md.mesh,'dimension'),
114 if md.mesh.dimension==2,
115 md.mesh=mesh2d(md.mesh);
116 else
117 md.mesh=mesh3dprisms(md.mesh);
118 end
119 else
120 md.mesh=mesh2dvertical(md.mesh);
121 end
122 end
123 %2014 November 12
124 if isa(md.calving,'double'); md.calving=calving(); end
125 %2016 February 3
126 if isa(md.slr,'double'); md.slr=slr(); 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=giaivins(); 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
152 end% }}}
153 end
154 methods
155 function md = model(varargin) % {{{
156
157 switch nargin
158 case 0
159 md=setdefaultparameters(md);
160 case 1
161 error('model constructor not supported yet');
162
163 otherwise
164 error('model constructor error message: 0 of 1 argument only in input.');
165 end
166 end
167 %}}}
168 function md = checkmessage(md,string) % {{{
169 if(nargout~=1) error('wrong usage, model must be an output'); end
170 disp(['model not consistent: ' string]);
171 md.private.isconsistent=false;
172 end
173 %}}}
174 function md = collapse(md)% {{{
175 %COLLAPSE - collapses a 3d mesh into a 2d mesh
176 %
177 % This routine collapses a 3d model into a 2d model
178 % and collapses all the fileds of the 3d model by
179 % taking their depth-averaged values
180 %
181 % Usage:
182 % md=collapse(md)
183 %
184 % See also: EXTRUDE, MODELEXTRACT
185
186 %Check that the model is really a 3d model
187 if ~strcmp(md.mesh.elementtype(),'Penta'),
188 error('collapse error message: only 3d mesh can be collapsed')
189 end
190
191 %Start with changing all the fields from the 3d mesh
192
193 %dealing with the friction law
194 %drag is limited to nodes that are on the bedrock.
195 if isa(md.friction,'friction'),
196 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
197 md.friction.p=project2d(md,md.friction.p,1);
198 md.friction.q=project2d(md,md.friction.q,1);
199 elseif isa(md.friction,'frictioncoulomb'),
200 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
201 md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1);
202 md.friction.p=project2d(md,md.friction.p,1);
203 md.friction.q=project2d(md,md.friction.q,1);
204 elseif isa(md.friction,'frictionhydro'),
205 md.friction.q=project2d(md,md.friction.q,1);
206 md.friction.C=project2d(md,md.friction.C,1);
207 md.friction.As=project2d(md,md.friction.As,1);
208 md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
209 elseif isa(md.friction,'frictionwaterlayer'),
210 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
211 md.friction.p=project2d(md,md.friction.p,1);
212 md.friction.q=project2d(md,md.friction.q,1);
213 md.friction.water_layer=project2d(md,md.friction.water_layer,1);
214 elseif isa(md.friction,'frictionweertman'),
215 md.friction.C=project2d(md,md.friction.C,1);
216 md.friction.m=project2d(md,md.friction.m,1);
217 elseif isa(md.friction,'frictionweertmantemp'),
218 md.friction.C=project2d(md,md.friction.C,1);
219 md.friction.m=project2d(md,md.friction.m,1);
220 else
221 disp('friction type not supported');
222 end
223
224 %observations
225 if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
226 if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
227 if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
228 if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
229 if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
230 if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
231 if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
232 md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
233 elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
234 md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
235 end;
236
237 %results
238 if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
239 if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
240 if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
241 if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
242 if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
243 if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
244 if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
245 if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
246 if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
247 if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
248 if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
249 %giaivins
250 if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
251 if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
252
253 %elementstype
254 if ~isnan(md.flowequation.element_equation)
255 md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
256 md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
257 md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
258 md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
259 md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
260 end
261
262 %boundary conditions
263 md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
264 md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
265 md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
266 md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
267 md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
268 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
269 if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
270 if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
271 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
272
273 % Hydrologydc variables
274 if isa(md.hydrology,'hydrologydc');
275 md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
276 md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
277 md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
278 md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
279 if(md.hydrology.isefficientlayer==1)
280 md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
281 end
282 end
283
284 %materials
285 md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
286 md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
287
288 %damage:
289 if md.damage.isdamage,
290 md.damage.D=DepthAverage(md,md.damage.D);
291 end
292
293 %special for thermal modeling:
294 if ~isnan(md.basalforcings.groundedice_melting_rate),
295 md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
296 end
297 if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
298 md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
299 end
300 md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
301
302 if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
303 md.calving.coeff=project2d(md,md.calving.coeff,1);
304 end
305 if isprop(md.calving,'meltingrate') & ~isnan(md.calving.meltingrate),
306 md.calving.meltingrate=project2d(md,md.calving.meltingrate,1);
307 end
308
309 %update of connectivity matrix
310 md.mesh.average_vertex_connectivity=25;
311
312 %Collapse the mesh
313 nodes2d=md.mesh.numberofvertices2d;
314 elements2d=md.mesh.numberofelements2d;
315
316 %parameters
317 md.geometry.surface=project2d(md,md.geometry.surface,1);
318 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
319 md.geometry.base=project2d(md,md.geometry.base,1);
320 if ~isnan(md.geometry.bed),
321 md.geometry.bed=project2d(md,md.geometry.bed,1);
322 end
323
324 if ~isnan(md.mask.groundedice_levelset),
325 md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
326 end
327 if ~isnan(md.mask.ice_levelset),
328 md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
329 end
330
331 %lat long
332 if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
333 if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
334
335 %outputdefinitions
336 for i=1:length(md.outputdefinition.definitions)
337 if isobject(md.outputdefinition.definitions{i})
338 %get subfields
339 solutionsubfields=fields(md.outputdefinition.definitions{i});
340 for j=1:length(solutionsubfields),
341 field=md.outputdefinition.definitions{i}.(solutionsubfields{j});
342 if length(field)==md.mesh.numberofvertices | length(field)==md.mesh.numberofelements,
343 md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1);
344 end
345 end
346 end
347 end
348
349 %Initialize with the 2d mesh
350 mesh=mesh2d();
351 mesh.x=md.mesh.x2d;
352 mesh.y=md.mesh.y2d;
353 mesh.numberofvertices=md.mesh.numberofvertices2d;
354 mesh.numberofelements=md.mesh.numberofelements2d;
355 mesh.elements=md.mesh.elements2d;
356 if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end
357 if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end
358 mesh.epsg=md.mesh.epsg;
359 if numel(md.mesh.scale_factor)==md.mesh.numberofvertices, mesh.scale_factor=project2d(md,md.mesh.scale_factor,1); end
360 if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
361 if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
362 md.mesh=mesh;
363 md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
364 md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
365 md.mesh.segments=contourenvelope(md.mesh);
366
367 end % }}}
368 function md2 = extract(md,area,varargin) % {{{
369 %extract - extract a model according to an Argus contour or flag list
370 %
371 % This routine extracts a submodel from a bigger model with respect to a given contour
372 % md must be followed by the corresponding exp file or flags list
373 % It can either be a domain file (argus type, .exp extension), or an array of element flags.
374 % If user wants every element outside the domain to be
375 % extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
376 % an empty string '' will be considered as an empty domain
377 % a string 'all' will be considered as the entire domain
378 %
379 % Usage:
380 % md2=extract(md,area);
381 %
382 % Examples:
383 % md2=extract(md,'Domain.exp');
384 %
385 % See also: EXTRUDE, COLLAPSE
386
387 %copy model
388 md1=md;
389
390 %recover optoins:
391 options=pairoptions(varargin{:});
392
393 %some checks
394 if ((nargin<2) | (nargout~=1)),
395 help extract
396 error('extract error message: bad usage');
397 end
398
399 %get elements that are inside area
400 flag_elem=FlagElements(md1,area);
401 if ~any(flag_elem),
402 error('extracted model is empty');
403 end
404
405 %kick out all elements with 3 dirichlets
406 if getfieldvalue(options,'spccheck',1)
407 spc_elem=find(~flag_elem);
408 spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
409 flag=ones(md1.mesh.numberofvertices,1);
410 flag(spc_node)=0;
411 pos=find(sum(flag(md1.mesh.elements),2)==0);
412 flag_elem(pos)=0;
413 end
414
415 %extracted elements and nodes lists
416 pos_elem=find(flag_elem);
417 pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
418
419 %keep track of some fields
420 numberofvertices1=md1.mesh.numberofvertices;
421 numberofelements1=md1.mesh.numberofelements;
422 numberofvertices2=length(pos_node);
423 numberofelements2=length(pos_elem);
424 flag_node=zeros(numberofvertices1,1);
425 flag_node(pos_node)=1;
426
427 %Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
428 Pelem=zeros(numberofelements1,1);
429 Pelem(pos_elem)=[1:numberofelements2]';
430 Pnode=zeros(numberofvertices1,1);
431 Pnode(pos_node)=[1:numberofvertices2]';
432
433 %renumber the elements (some nodes won't exist anymore)
434 elements_1=md1.mesh.elements;
435 elements_2=elements_1(pos_elem,:);
436 elements_2(:,1)=Pnode(elements_2(:,1));
437 elements_2(:,2)=Pnode(elements_2(:,2));
438 elements_2(:,3)=Pnode(elements_2(:,3));
439 if isa(md1.mesh,'mesh3dprisms'),
440 elements_2(:,4)=Pnode(elements_2(:,4));
441 elements_2(:,5)=Pnode(elements_2(:,5));
442 elements_2(:,6)=Pnode(elements_2(:,6));
443 end
444
445 %OK, now create the new model!
446
447 %take every field from model
448 md2=md1;
449
450 %automatically modify fields
451
452 %loop over model fields
453 model_fields=fields(md1);
454 for i=1:length(model_fields),
455 %get field
456 field=md1.(model_fields{i});
457 fieldsize=size(field);
458 if isobject(field), %recursive call
459 object_fields=fields(md1.(model_fields{i}));
460 for j=1:length(object_fields),
461 %get field
462 field=md1.(model_fields{i}).(object_fields{j});
463 fieldsize=size(field);
464 %size = number of nodes * n
465 if fieldsize(1)==numberofvertices1
466 md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
467 elseif (fieldsize(1)==numberofvertices1+1)
468 md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
469 %size = number of elements * n
470 elseif fieldsize(1)==numberofelements1
471 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
472 elseif (fieldsize(1)==numberofelements1+1)
473 md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
474 end
475 end
476 else
477 %size = number of nodes * n
478 if fieldsize(1)==numberofvertices1
479 md2.(model_fields{i})=field(pos_node,:);
480 elseif (fieldsize(1)==numberofvertices1+1)
481 md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
482 %size = number of elements * n
483 elseif fieldsize(1)==numberofelements1
484 md2.(model_fields{i})=field(pos_elem,:);
485 elseif (fieldsize(1)==numberofelements1+1)
486 md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
487 end
488 end
489 end
490
491 %modify some specific fields
492
493 %Mesh
494 md2.mesh.numberofelements=numberofelements2;
495 md2.mesh.numberofvertices=numberofvertices2;
496 md2.mesh.elements=elements_2;
497
498 %mesh.uppervertex mesh.lowervertex
499 if isa(md1.mesh,'mesh3dprisms'),
500 md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
501 pos=find(~isnan(md2.mesh.uppervertex));
502 md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
503
504 md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
505 pos=find(~isnan(md2.mesh.lowervertex));
506 md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
507
508 md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
509 pos=find(~isnan(md2.mesh.upperelements));
510 md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
511
512 md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
513 pos=find(~isnan(md2.mesh.lowerelements));
514 md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
515 end
516
517 %Initial 2d mesh
518 if isa(md1.mesh,'mesh3dprisms'),
519 flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
520 pos_elem_2d=find(flag_elem_2d);
521 flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
522 pos_node_2d=find(flag_node_2d);
523
524 md2.mesh.numberofelements2d=length(pos_elem_2d);
525 md2.mesh.numberofvertices2d=length(pos_node_2d);
526 md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
527 md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
528 md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
529 md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
530
531 md2.mesh.x2d=md1.mesh.x(pos_node_2d);
532 md2.mesh.y2d=md1.mesh.y(pos_node_2d);
533 end
534
535 %Edges
536 if(dimension(md.mesh)==2),
537 if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
538 %renumber first two columns
539 pos=find(md2.mesh.edges(:,4)~=-1);
540 md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
541 md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
542 md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
543 md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
544 %remove edges when the 2 vertices are not in the domain.
545 md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
546 %Replace all zeros by -1 in the last two columns
547 pos=find(md2.mesh.edges(:,3)==0);
548 md2.mesh.edges(pos,3)=-1;
549 pos=find(md2.mesh.edges(:,4)==0);
550 md2.mesh.edges(pos,4)=-1;
551 %Invert -1 on the third column with last column (Also invert first two columns!!)
552 pos=find(md2.mesh.edges(:,3)==-1);
553 md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
554 md2.mesh.edges(pos,4)=-1;
555 values=md2.mesh.edges(pos,2);
556 md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
557 md2.mesh.edges(pos,1)=values;
558 %Finally remove edges that do not belong to any element
559 pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
560 md2.mesh.edges(pos,:)=[];
561 end
562 end
563
564 %Penalties
565 if ~isnan(md2.stressbalance.vertex_pairing),
566 for i=1:size(md1.stressbalance.vertex_pairing,1);
567 md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
568 end
569 md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
570 end
571 if ~isnan(md2.masstransport.vertex_pairing),
572 for i=1:size(md1.masstransport.vertex_pairing,1);
573 md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
574 end
575 md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
576 end
577
578 %recreate segments
579 if isa(md1.mesh,'mesh2d') | isa(md1.mesh','mesh3dsurface'),
580 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
581 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
582 md2.mesh.segments=contourenvelope(md2.mesh);
583 md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
584 else
585 %First do the connectivity for the contourenvelope in 2d
586 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
587 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
588 segments=contourenvelope(md2.mesh);
589 md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
590 md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
591 %Then do it for 3d as usual
592 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
593 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
594 end
595
596 %Boundary conditions: Dirichlets on new boundary
597 %Catch the elements that have not been extracted
598 orphans_elem=find(~flag_elem);
599 orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
600 %Figure out which node are on the boundary between md2 and md1
601 nodestoflag1=intersect(orphans_node,pos_node);
602 nodestoflag2=Pnode(nodestoflag1);
603 if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
604 if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
605 md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
606 md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
607 else
608 md2.stressbalance.spcvx(nodestoflag2)=NaN;
609 md2.stressbalance.spcvy(nodestoflag2)=NaN;
610 disp(' ')
611 disp('!! extract warning: spc values should be checked !!')
612 disp(' ')
613 end
614 %put 0 for vz
615 md2.stressbalance.spcvz(nodestoflag2)=0;
616 end
617 if ~isnan(md1.thermal.spctemperature),
618 md2.thermal.spctemperature(nodestoflag2,1)=1;
619 end
620
621 %Results fields
622 if isstruct(md1.results),
623 md2.results=struct();
624 solutionfields=fields(md1.results);
625 for i=1:length(solutionfields),
626 if isstruct(md1.results.(solutionfields{i}))
627 %get subfields
628 solutionsubfields=fields(md1.results.(solutionfields{i}));
629 for j=1:length(solutionsubfields),
630 field=md1.results.(solutionfields{i}).(solutionsubfields{j});
631 if length(field)==numberofvertices1,
632 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
633 elseif length(field)==numberofelements1,
634 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
635 else
636 md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
637 end
638 end
639 else
640 field=md1.results.(solutionfields{i});
641 if length(field)==numberofvertices1,
642 md2.results.(solutionfields{i})=field(pos_node);
643 elseif length(field)==numberofelements1,
644 md2.results.(solutionfields{i})=field(pos_elem);
645 else
646 md2.results.(solutionfields{i})=field;
647 end
648 end
649 end
650 end
651
652 %OutputDefinitions fields
653 for i=1:length(md1.outputdefinition.definitions),
654 if isobject(md1.outputdefinition.definitions{i})
655 %get subfields
656 solutionsubfields=fields(md1.outputdefinition.definitions{i});
657 for j=1:length(solutionsubfields),
658 field=md1.outputdefinition.definitions{i}.(solutionsubfields{j});
659 if length(field)==numberofvertices1,
660 md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node);
661 elseif length(field)==numberofelements1,
662 md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem);
663 end
664 end
665 end
666 end
667
668 %Keep track of pos_node and pos_elem
669 md2.mesh.extractedvertices=pos_node;
670 md2.mesh.extractedelements=pos_elem;
671 end % }}}
672 function md = extrude(md,varargin) % {{{
673 %EXTRUDE - vertically extrude a 2d mesh
674 %
675 % vertically extrude a 2d mesh and create corresponding 3d mesh.
676 % The vertical distribution can:
677 % - follow a polynomial law
678 % - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
679 % - be discribed by a list of coefficients (between 0 and 1)
680 %
681 %
682 % Usage:
683 % md=extrude(md,numlayers,extrusionexponent);
684 % md=extrude(md,numlayers,lowerexponent,upperexponent);
685 % md=extrude(md,listofcoefficients);
686 %
687 % Example:
688 % md=extrude(md,15,1.3);
689 % md=extrude(md,15,1.3,1.2);
690 % md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
691 %
692 % See also: MODELEXTRACT, COLLAPSE
693
694 %some checks on list of arguments
695 if ((nargin>4) | (nargin<2) | (nargout~=1)),
696 help extrude;
697 error('extrude error message');
698 end
699
700 %Extrude the mesh
701 if nargin==2, %list of coefficients
702 clist=varargin{1};
703 if any(clist<0) | any(clist>1),
704 error('extrusioncoefficients must be between 0 and 1');
705 end
706 extrusionlist=sort(unique([clist(:);0;1]));
707 numlayers=length(extrusionlist);
708 elseif nargin==3, %one polynomial law
709 if varargin{2}<=0,
710 help extrude;
711 error('extrusionexponent must be >=0');
712 end
713 numlayers=varargin{1};
714 extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
715 elseif nargin==4, %two polynomial laws
716 numlayers=varargin{1};
717 lowerexp=varargin{2};
718 upperexp=varargin{3};
719
720 if varargin{2}<=0 | varargin{3}<=0,
721 help extrude;
722 error('lower and upper extrusionexponents must be >=0');
723 end
724
725 lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
726 upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
727 extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
728
729 end
730
731 if numlayers<2,
732 error('number of layers should be at least 2');
733 end
734 if strcmp(md.mesh.domaintype(),'3D')
735 error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
736 end
737
738 %Initialize with the 2d mesh
739 mesh2d = md.mesh;
740 md.mesh=mesh3dprisms();
741 md.mesh.x = mesh2d.x;
742 md.mesh.y = mesh2d.y;
743 md.mesh.elements = mesh2d.elements;
744 md.mesh.numberofelements = mesh2d.numberofelements;
745 md.mesh.numberofvertices = mesh2d.numberofvertices;
746
747 md.mesh.lat = mesh2d.lat;
748 md.mesh.long = mesh2d.long;
749 md.mesh.epsg = mesh2d.epsg;
750 md.mesh.scale_factor = mesh2d.scale_factor;
751
752 md.mesh.vertexonboundary = mesh2d.vertexonboundary;
753 md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
754 md.mesh.elementconnectivity = mesh2d.elementconnectivity;
755 md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
756
757 md.mesh.extractedvertices = mesh2d.extractedvertices;
758 md.mesh.extractedelements = mesh2d.extractedelements;
759
760 x3d=[];
761 y3d=[];
762 z3d=[]; %the lower node is on the bed
763 thickness3d=md.geometry.thickness; %thickness and bed for these nodes
764 bed3d=md.geometry.base;
765
766 %Create the new layers
767 for i=1:numlayers,
768 x3d=[x3d; md.mesh.x];
769 y3d=[y3d; md.mesh.y];
770 %nodes are distributed between bed and surface accordingly to the given exponent
771 z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
772 end
773 number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
774
775 %Extrude elements
776 elements3d=[];
777 for i=1:numlayers-1,
778 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
779 end
780 number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
781
782 %Keep a trace of lower and upper nodes
783 lowervertex=NaN*ones(number_nodes3d,1);
784 uppervertex=NaN*ones(number_nodes3d,1);
785 lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
786 uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
787 md.mesh.lowervertex=lowervertex;
788 md.mesh.uppervertex=uppervertex;
789
790 %same for lower and upper elements
791 lowerelements=NaN*ones(number_el3d,1);
792 upperelements=NaN*ones(number_el3d,1);
793 lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
794 upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
795 md.mesh.lowerelements=lowerelements;
796 md.mesh.upperelements=upperelements;
797
798 %Save old mesh
799 md.mesh.x2d=md.mesh.x;
800 md.mesh.y2d=md.mesh.y;
801 md.mesh.elements2d=md.mesh.elements;
802 md.mesh.numberofelements2d=md.mesh.numberofelements;
803 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
804
805 %Build global 3d mesh
806 md.mesh.elements=elements3d;
807 md.mesh.x=x3d;
808 md.mesh.y=y3d;
809 md.mesh.z=z3d;
810 md.mesh.numberofelements=number_el3d;
811 md.mesh.numberofvertices=number_nodes3d;
812 md.mesh.numberoflayers=numlayers;
813
814 %Ok, now deal with the other fields from the 2d mesh:
815
816 %bedinfo and surface info
817 md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
818 md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
819 md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
820
821 %lat long
822 md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
823 md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
824 md.mesh.scale_factor=project3d(md,'vector',md.mesh.scale_factor,'type','node');
825
826 md.geometry=extrude(md.geometry,md);
827 md.friction = extrude(md.friction,md);
828 md.inversion = extrude(md.inversion,md);
829 md.smb = extrude(md.smb,md);
830 md.initialization = extrude(md.initialization,md);
831
832 md.flowequation=md.flowequation.extrude(md);
833 md.stressbalance=extrude(md.stressbalance,md);
834 md.thermal=md.thermal.extrude(md);
835 md.masstransport=md.masstransport.extrude(md);
836 md.levelset=extrude(md.levelset,md);
837 md.calving=extrude(md.calving,md);
838 md.hydrology = extrude(md.hydrology,md);
839 md.slr = extrude(md.slr,md);
840
841 %connectivity
842 if ~isnan(md.mesh.elementconnectivity)
843 md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
844 md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
845 for i=2:numlayers-1,
846 md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
847 =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
848 end
849 md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
850 end
851
852 md.materials=extrude(md.materials,md);
853 md.damage=extrude(md.damage,md);
854 md.mask=extrude(md.mask,md);
855 md.qmu=extrude(md.qmu,md);
856 md.basalforcings=extrude(md.basalforcings,md);
857 md.outputdefinition=extrude(md.outputdefinition,md);
858
859 %increase connectivity if less than 25:
860 if md.mesh.average_vertex_connectivity<=25,
861 md.mesh.average_vertex_connectivity=100;
862 end
863 end % }}}
864 function md = structtomodel(md,structmd) % {{{
865
866 if ~isstruct(structmd) error('input model is not a structure'); end
867
868 %loaded model is a struct, initialize output and recover all fields
869 md = structtoobj(model,structmd);
870
871 %Old field now classes
872 if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
873 if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
874
875 %Field name change
876 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
877 if isfield(structmd,'p'), md.friction.p=structmd.p; end
878 if isfield(structmd,'q'), md.friction.q=structmd.p; end
879 if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
880 if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
881 if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
882 if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
883 if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
884 if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
885 if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
886 if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
887 if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
888 if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
889 if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
890 if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
891 if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
892 if isfield(structmd,'g'), md.constants.g=structmd.g; end
893 if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
894 if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
895 if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
896 if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
897 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
898 if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
899 if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
900 if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
901 if isfield(structmd,'riftproperties'), %old implementation
902 md.rifts=rifts();
903 md.rifts.riftproperties=structmd.riftproperties;
904 md.rifts.riftstruct=structmd.rifts;
905 md.rifts.riftproperties=structmd.riftinfo;
906 end
907 if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
908 if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
909 if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
910 if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
911 if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
912 if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
913 if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
914 if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
915 if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
916 if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
917 if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
918 if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
919 if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
920 if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
921 if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
922 if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
923 if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
924 if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
925 if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
926 if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
927 if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
928 if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
929 if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
930 if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
931 if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
932 if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
933 if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
934 if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
935 if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
936 if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
937 if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
938 if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
939 if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
940 if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
941 if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
942 if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
943 if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
944 if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
945 if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
946 if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
947 if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
948 if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
949 if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
950 if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
951 if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
952 if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
953 if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
954 if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
955 if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
956 if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
957 if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
958 if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
959 if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
960 if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
961 if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
962 if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
963 if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
964 if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
965 if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
966 if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
967 if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
968 if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
969 if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
970 if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
971 if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
972 if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
973 if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
974 if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
975 if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
976 if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
977 if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
978 if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
979 if isfield(structmd,'long'), md.mesh.long=structmd.long; end
980 if isfield(structmd,'scale_factor'), md.mesh.scale_factor=structmd.scale_factor; end
981 if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
982 if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
983 if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
984 if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
985 if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
986 if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
987 if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
988 if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
989 if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
990 if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
991 if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
992 if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
993 if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
994 if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
995 if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
996 if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
997 if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
998 if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
999 if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
1000 if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
1001 if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
1002 if isfield(structmd,'edges'),
1003 md.mesh.edges=structmd.edges;
1004 md.mesh.edges(isnan(md.mesh.edges))=-1;
1005 end
1006 if isfield(structmd,'y'), md.mesh.y=structmd.y; end
1007 if isfield(structmd,'x'), md.mesh.x=structmd.x; end
1008 if isfield(structmd,'z'), md.mesh.z=structmd.z; end
1009 if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
1010 if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
1011 if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
1012
1013 if isnumeric(md.verbose),
1014 md.verbose=verbose;
1015 end
1016
1017 if isfield(structmd,'spcvelocity'),
1018 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
1019 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
1020 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1021 pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
1022 pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
1023 pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
1024 end
1025 if isfield(structmd,'spcvx'),
1026 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
1027 pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
1028 end
1029 if isfield(structmd,'spcvy'),
1030 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
1031 pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
1032 end
1033 if isfield(structmd,'spcvz'),
1034 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1035 pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
1036 end
1037 if isfield(structmd,'pressureload'),
1038 if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
1039 pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
1040 pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
1041 pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
1042 end
1043 end
1044 if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
1045 pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
1046 pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
1047 pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
1048 pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
1049 pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
1050 pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
1051 pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
1052 pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
1053 end
1054 if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
1055 pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
1056 pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
1057 pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
1058 pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
1059 pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
1060 pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
1061 pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
1062 pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
1063 end
1064 if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
1065 if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
1066 if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1067 if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1068 end
1069 if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1070 if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1071 if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
1072 if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1073 end
1074 if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1075 if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1076 if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1077 if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1078 end
1079 if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1080 pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1081 pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1082 pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1083 pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1084 pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1085 pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1086 pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1087 pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1088 pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1089 end
1090
1091 if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1092 md.thermal.stabilization=2;
1093 md.masstransport.stabilization=1;
1094 md.balancethickness.stabilization=1;
1095 end
1096 if isnumeric(md.masstransport.hydrostatic_adjustment)
1097 if md.masstransport.hydrostatic_adjustment==269,
1098 md.masstransport.hydrostatic_adjustment='Incremental';
1099 else
1100 md.masstransport.hydrostatic_adjustment='Absolute';
1101 end
1102 end
1103
1104 %New fields
1105 if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
1106 md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1107 md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1108 end
1109 if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
1110 md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1111 md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1112 end
1113 if ~isfield(structmd,'diagnostic_ref');
1114 md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1115 end
1116 if ~isfield(structmd,'loadingforce');
1117 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1118 end
1119
1120 %2013 August 9
1121 if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1122 disp('Recovering old prognostic class');
1123 md.masstransport=masstransport(structmd.prognostic);
1124 end
1125 %2013 August 9
1126 if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') || isa(structmd.diagnostic,'stressbalance')),
1127 disp('Recovering old diagnostic class');
1128 md.stressbalance=stressbalance(structmd.diagnostic);
1129 end
1130 %2014 January 9th
1131 if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
1132 disp('Recovering old surfaceforcings class');
1133 mass_balance=structmd.surfaceforcings.mass_balance;
1134 md.smb=SMB();
1135 md.smb.mass_balance=mass_balance;
1136 end
1137 %2015 September 10
1138 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
1139 disp('Recovering old SMB class');
1140 md.smb=SMBforcing(structmd.surfaceforcings);
1141 end
1142 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
1143 disp('Recovering old SMBhenning class');
1144 md.smb=SMBhenning(structmd.surfaceforcings);
1145 end
1146
1147 end% }}}
1148 function md = setdefaultparameters(md) % {{{
1149
1150 %initialize subclasses
1151 md.mesh = mesh2d();
1152 md.mask = mask();
1153 md.constants = constants();
1154 md.geometry = geometry();
1155 md.initialization = initialization();
1156 md.smb = SMBforcing();
1157 md.basalforcings = basalforcings();
1158 md.friction = friction();
1159 md.rifts = rifts();
1160 md.slr = slr();
1161 md.timestepping = timestepping();
1162 md.groundingline = groundingline();
1163 md.materials = matice();
1164 md.damage = damage();
1165 md.flowequation = flowequation();
1166 md.debug = debug();
1167 md.verbose = verbose();
1168 md.settings = issmsettings();
1169 md.toolkits = toolkits();
1170 md.cluster = generic();
1171 md.balancethickness = balancethickness();
1172 md.stressbalance = stressbalance();
1173 md.hydrology = hydrologyshreve();
1174 md.masstransport = masstransport();
1175 md.thermal = thermal();
1176 md.steadystate = steadystate();
1177 md.transient = transient();
1178 md.levelset = levelset();
1179 md.calving = calving();
1180 md.gia = giaivins();
1181 md.esa = esa();
1182 md.love = fourierlove();
1183 md.esa = esa();
1184 md.autodiff = autodiff();
1185 md.inversion = inversion();
1186 md.qmu = qmu();
1187 md.amr = amr();
1188 md.radaroverlay = radaroverlay();
1189 md.results = struct();
1190 md.outputdefinition = outputdefinition();
1191 md.miscellaneous = miscellaneous();
1192 md.private = private();
1193 end
1194 %}}}
1195 function md = tetras(md,varargin) % {{{
1196 %TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1197 %
1198 % Usage:
1199 % md=tetra(md)
1200
1201 if ~isa(md.mesh,'mesh3dprisms')
1202 error('mesh is not a 3d prismatic mesh');
1203 end
1204
1205 %Initialize tetra mesh
1206 md.mesh=mesh3dtetras(md.mesh);
1207
1208 %Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
1209 steiner = 0;
1210 nbv = md.mesh.numberofvertices;
1211 nbt = 3*md.mesh.numberofelements;
1212 elements = zeros(nbt,4);
1213 for i=1:md.mesh.numberofelements
1214 v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
1215 v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
1216 if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1217 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1218 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1219 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1220 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1221 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1222 elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
1223 elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
1224 elements(end+1,:) = [v2 v3 v5 v7];
1225 elements(end+1,:) = [v3 v5 v6 v7];
1226 elements(end+1,:) = [v1 v3 v6 v7];
1227 elements(end+1,:) = [v1 v4 v6 v7];
1228 elements(end+1,:) = [v4 v5 v6 v7];
1229 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1230 elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
1231 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1232 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1233 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1234 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1235 elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
1236 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1237 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1238 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1239 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1240 elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
1241 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1242 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1243 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1244 elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
1245 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1246 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1247 elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
1248 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1249 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1250 elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
1251 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1252 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1253 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1254 elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
1255 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1256 elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
1257 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1258 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1259 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1260 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1261 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1262 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1263 elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
1264 elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
1265 elements(end+1,:) = [v2 v5 v6 v7];
1266 elements(end+1,:) = [v2 v3 v6 v7];
1267 elements(end+1,:) = [v3 v4 v6 v7];
1268 elements(end+1,:) = [v1 v3 v4 v7];
1269 elements(end+1,:) = [v4 v5 v6 v7];
1270 else
1271 error('Case not supported'); %not supposed to happen!
1272 end
1273 %Reorder elements to make sure they are direct
1274 for j=1:3
1275 element = elements(3*(i-1)+j,:);
1276 matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
1277 if det(matrix)>0,
1278 elements(3*(i-1)+j,1)=element(2);
1279 elements(3*(i-1)+j,2)=element(1);
1280 end
1281 end
1282 end
1283 %%Split in 3 tetras
1284 %subelement1 = [1 2 3 5];
1285 %subelement2 = [4 6 5 1];
1286 %subelement3 = [5 6 3 1];
1287 %elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
1288 if steiner==0,
1289 disp('No Steiner point required to split prismatic mesh into tets');
1290 else
1291 disp([num2str(steiner) ' Steiner points had to be included'])
1292 error('Steiner point not supported yet');
1293 end
1294
1295 pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1296
1297 md.mesh.elements=elements;
1298 md.mesh.numberofelements=size(elements,1);
1299
1300 %p and q (same deal, except for element that are on the bedrock: )
1301 if ~isnan(md.friction.p),
1302 md.friction.p=md.friction.p(pos_elements);
1303 md.friction.q=md.friction.q(pos_elements);
1304 end
1305
1306 %elementstype
1307 if ~isnan(md.flowequation.element_equation)
1308 oldelements_type=md.flowequation.element_equation;
1309 md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1310 end
1311
1312 %connectivity
1313 md.mesh.elementconnectivity=NaN;
1314
1315 %materials
1316 if ~isnan(md.materials.rheology_n),
1317 md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1318 end
1319
1320 %increase connectivity if less than 25:
1321 if md.mesh.average_vertex_connectivity<=25,
1322 md.mesh.average_vertex_connectivity=100;
1323 end
1324 end % }}}
1325 function disp(self) % {{{
1326 disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
1327 disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
1328 disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1329 disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
1330 disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
1331 disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
1332 disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
1333 disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
1334 disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
1335 disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
1336 disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
1337 disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
1338 disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
1339 disp(sprintf('%19s: %-22s -- %s','slr' ,['[1x1 ' class(self.slr) ']'],'slr forcings'));
1340 disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
1341 disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
1342 disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
1343 disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
1344 disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
1345 disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
1346 disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
1347 disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
1348 disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
1349 disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
1350 disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
1351 disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
1352 disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
1353 disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
1354 disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
1355 disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
1356 disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
1357 disp(sprintf('%19s: %-22s -- %s','love' ,['[1x1 ' class(self.love) ']'],'parameters for love solution'));
1358 disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
1359 disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
1360 disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
1361 disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
1362 disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
1363 disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
1364 disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
1365 disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
1366 end % }}}
1367 function memory(self) % {{{
1368
1369 disp(sprintf('\nMemory imprint:\n'));
1370
1371 fields=properties('model');
1372 mem=0;
1373
1374 for i=1:length(fields),
1375 field=self.(fields{i});
1376 s=whos('field');
1377 mem=mem+s.bytes/1e6;
1378 disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1379 end
1380 disp(sprintf('%19s--%10s','--------------','--------------'));
1381 disp(sprintf('%19s: %g Mb','Total',mem));
1382 end % }}}
1383 function netcdf(self,filename) % {{{
1384 %NETCDF - save model as netcdf
1385 %
1386 % Usage:
1387 % netcdf(md,filename)
1388 %
1389 % Example:
1390 % netcdf(md,'model.nc');
1391
1392 disp('Saving model as NetCDF');
1393 %1. Create NetCDF file
1394 ncid=netcdf.create(filename,'CLOBBER');
1395 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1396 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
1397 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1398 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1399
1400 %Preallocate variable id, needed to write variables in netcdf file
1401 var_id=zeros(1000,1);%preallocate
1402
1403 for step=1:2,
1404 counter=0;
1405 [var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
1406 if step==1, netcdf.endDef(ncid); end
1407 end
1408
1409 if counter>1000,
1410 warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1411 end
1412
1413 netcdf.close(ncid)
1414 end % }}}
1415 function xylim(self) % {{{
1416
1417 xlim([min(self.mesh.x) max(self.mesh.x)]);
1418 ylim([min(self.mesh.y) max(self.mesh.y)])
1419 end % }}}
1420 function md=upload(md) % {{{
1421 %the goal of this routine is to upload the model onto a server, and to empty it.
1422 %So first, save the model with a unique name and upload the file to the server:
1423 random_part=fix(rand(1)*10000);
1424 id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1425 eval(['save ' id ' md']);
1426
1427 %Now, upload the file:
1428 issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1429
1430 %Now, empty this model of everything except settings, and record name of file we just uploaded!
1431 settings_back=md.settings;
1432 md=model();
1433 md.settings=settings_back;
1434 md.settings.upload_filename=id;
1435
1436 %get locally rid of file that was uploaded
1437 eval(['delete ' id]);
1438
1439 end % }}}
1440 function md=download(md) % {{{
1441
1442 %the goal of this routine is to download the internals of the current model from a server, because
1443 %this model is empty, except for the settings which tell us where to go and find this model!
1444
1445 %Download the file:
1446 issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1447
1448 name=md.settings.upload_filename;
1449
1450 %Now, load this model:
1451 md=loadmodel(md.settings.upload_filename);
1452
1453 %get locally rid of file that was downloaded
1454 eval(['delete ' name]);
1455
1456 end % }}}
1457 function savemodeljs(md,modelname,websiteroot,varargin) % {{{
1458
1459 %the goal of this routine is to save the model as a javascript array that can be included in any html
1460 %file:
1461
1462 options=pairoptions(varargin{:});
1463 optimization=getfieldvalue(options,'optimize',0);
1464
1465
1466 %disp:
1467 disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
1468
1469 %open file for writing and declare the model:
1470 fid=fopen([websiteroot '/js/' modelname '.js'],'w');
1471 fprintf(fid,'var %s=new model();\n',modelname);
1472
1473 %now go through all the classes and fwrite all the corresponding fields:
1474
1475 fields=properties('model');
1476 for i=1:length(fields),
1477 field=fields{i};
1478
1479 %Some properties do not need to be saved
1480 if ismember(field,{'results','cluster' }),
1481 continue;
1482 end
1483
1484 %some optimization:
1485 if optimization==1,
1486 %optimize for plotting only:
1487 if ~ismember(field,{'geometry','mesh','mask'}),
1488 continue;
1489 end
1490 end
1491
1492 %Check that current field is an object
1493 if ~isobject(md.(field))
1494 error(['field ''' char(field) ''' is not an object']);
1495 end
1496
1497 %savemodeljs for current object
1498 %disp(['javascript saving ' field '...']);
1499 savemodeljs(md.(field),fid,modelname);
1500 end
1501
1502 %done, close file:
1503 fclose(fid);
1504 end
1505 end
1506 end
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