source: issm/trunk-jpl/src/m/classes/model.m@ 18506

Last change on this file since 18506 was 18506, checked in by bdef, 11 years ago

BUG: adding seaice field if nonexistent, collapsing Hydrology
File size: 67.6 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 surfaceforcings = 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
25 debug = 0;
26 verbose = 0;
27 settings = 0;
28 toolkits = 0;
29 cluster = 0;
30
31 balancethickness = 0;
32 stressbalance = 0;
33 groundingline = 0;
34 hydrology = 0;
35 masstransport = 0;
36 thermal = 0;
37 steadystate = 0;
38 transient = 0;
39 gia = 0;
40
41 seaice = 0;
42
43 autodiff = 0;
44 flaim = 0;
45 inversion = 0;
46 qmu = 0;
47
48 results = 0;
49 outputdefinition = 0;
50 radaroverlay = 0;
51 miscellaneous = 0;
52 private = 0;
53
54 %}}}
55 end
56 methods (Static)
57 function md = loadobj(md) % {{{
58 % This function is directly called by matlab when a model object is
59 % loaded. If the input is a struct it is an old version of model and
60 % old fields must be recovered (make sure they are in the deprecated
61 % model properties)
62
63 if verLessThan('matlab','7.9'),
64 disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
65 disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
66
67 % This is a Matlab bug: all the fields of md have their default value
68 % Example of error message:
69 % Warning: Error loading an object of class 'model':
70 % Undefined function or method 'exist' for input arguments of type 'cell'
71 %
72 % This has been fixed in MATLAB 7.9 (R2009b) and later versions
73 end
74
75 if isstruct(md)
76 disp('Recovering model object from a previous version');
77 md = structtomodel(model,md);
78 end
79
80 %2012 August 4th
81 if isa(md.materials,'materials'),
82 disp('Recovering old materials');
83 if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
84 md.materials=matice(md.materials);
85 else
86 md.materials=matdamageice(md.materials);
87 end
88 end
89 %2013 April 12
90 if numel(md.stressbalance.loadingforce==1)
91 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
92 end
93 %2013 April 17
94 if isa(md.hydrology,'hydrology'),
95 disp('Recovering old hydrology class');
96 md.hydrology=hydrologyshreve(md.materials);
97 end
98 %2013 October 9
99 if ~isa(md.damage,'damage'),
100 md.damage=damage();
101 md.damage.D=zeros(md.mesh.numberofvertices,1);
102 md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
103 end
104 %2013 November 18
105 if ~isa(md.outputdefinition,'outputdefinition'),
106 md.outputdefinition=outputdefinition();
107 end
108 %2014 January 9th
109 if isa(md.surfaceforcings,'surfaceforcings'),
110 disp('Recovering old surfaceforcings class');
111 mass_balance=md.surfaceforcings.mass_balance;
112 md.surfaceforcings=SMB();
113 md.surfaceforcings.mass_balance=mass_balance;
114 end
115 %2014 March 26th
116 if isa(md.mesh,'mesh'),
117 disp('Recovering old mesh class');
118 if isprop(md.mesh,'dimension'),
119 if md.mesh.dimension==2,
120 md.mesh=mesh2d(md.mesh);
121 else
122 md.mesh=mesh3dprisms(md.mesh);
123 end
124 else
125 md.mesh=mesh2dvertical(md.mesh);
126 end
127 end
128 %2014 September 11
129 if (size(setdiff(fieldnames(md),'seaice'),1)==size(fieldnames(md),1));
130 md.seaice=seaice()
131 end
132 end% }}}
133 end
134 methods
135 function md = model(varargin) % {{{
136
137 switch nargin
138 case 0
139 md=setdefaultparameters(md);
140 case 1
141 if strcmpi(varargin{1},'seaice'),
142 md=setdefaultparameters(md);
143
144 %Specific subject for sea ice model
145 md.materials = matseaice();
146 md.surfaceforcings = seaiceatm();
147 md.basalforcings = seaiceocean();
148 md.initialization = seaiceinitialization();
149
150 %Change some of the defauls
151 md.timestepping.in_years = false;
152 md.constants.g = 9.80616; %Same as TOPAZ
153 else
154 error('model constructor not supported yet');
155 end
156
157 otherwise
158 error('model constructor error message: 0 of 1 argument only in input.');
159 end
160 end
161 %}}}
162 function md = checkmessage(md,string) % {{{
163 if(nargout~=1) error('wrong usage, model must be an output'); end
164 disp(['model not consistent: ' string]);
165 md.private.isconsistent=false;
166 end
167 %}}}
168 function md = collapse(md)% {{{
169 %COLLAPSE - collapses a 3d mesh into a 2d mesh
170 %
171 % This routine collapses a 3d model into a 2d model
172 % and collapses all the fileds of the 3d model by
173 % taking their depth-averaged values
174 %
175 % Usage:
176 % md=collapse(md)
177 %
178 % See also: EXTRUDE, MODELEXTRACT
179
180 %Check that the model is really a 3d model
181 if ~strcmp(md.mesh.elementtype(),'Penta'),
182 error('collapse error message: only 3d mesh can be collapsed')
183 end
184
185 %Start with changing all the fields from the 3d mesh
186
187 %drag is limited to nodes that are on the bedrock.
188 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
189
190 %p and q (same deal, except for element that are on the bedrock: )
191 md.friction.p=project2d(md,md.friction.p,1);
192 md.friction.q=project2d(md,md.friction.q,1);
193
194 %observations
195 if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
196 if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
197 if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
198 if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
199 if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
200 if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
201 if ~isnan(md.surfaceforcings.mass_balance),
202 md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers);
203 end;
204 if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
205
206 %results
207 if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
208 if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
209 if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
210 if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
211 if ~isnan(md.initialization.temperature), md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
212 if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
213
214 %gia
215 if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
216 if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
217
218 %elementstype
219 if ~isnan(md.flowequation.element_equation)
220 md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
221 md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
222 md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
223 md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
224 md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
225 end
226
227 %boundary conditions
228 md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
229 md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
230 md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
231 md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
232 md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
233 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
234 if ~isnan(md.damage.spcdamage), md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
235 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
236
237 % Hydrologydc variables
238 if isa(md.hydrology,'hydrologydc');
239 md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
240 md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
241 md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
242 md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
243 if(md.hydrology.isefficientlayer==1)
244 md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
245 end
246 end
247
248 %materials
249 md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
250 md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
251
252 %damage:
253 if md.damage.isdamage,
254 md.damage.D=DepthAverage(md,md.damage.D);
255 end
256
257 %special for thermal modeling:
258 if ~isnan(md.basalforcings.groundedice_melting_rate),
259 md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
260 end
261 if ~isnan(md.basalforcings.floatingice_melting_rate),
262 md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
263 end
264 md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
265
266 %update of connectivity matrix
267 md.mesh.average_vertex_connectivity=25;
268
269 %Collapse the mesh
270 nodes2d=md.mesh.numberofvertices2d;
271 elements2d=md.mesh.numberofelements2d;
272
273 %parameters
274 md.geometry.surface=project2d(md,md.geometry.surface,1);
275 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
276 md.geometry.base=project2d(md,md.geometry.base,1);
277 if ~isnan(md.geometry.bed),
278 md.geometry.bed=project2d(md,md.geometry.bed,1);
279 end
280
281 if ~isnan(md.mask.groundedice_levelset),
282 md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
283 end
284 if ~isnan(md.mask.ice_levelset),
285 md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
286 end
287
288 %lat long
289 if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
290 if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
291
292 %Initialize with the 2d mesh
293 mesh=mesh2d();
294 mesh.x=md.mesh.x2d;
295 mesh.y=md.mesh.y2d;
296 mesh.numberofvertices=md.mesh.numberofvertices2d;
297 mesh.numberofelements=md.mesh.numberofelements2d;
298 mesh.elements=md.mesh.elements2d;
299 if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
300 if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
301 md.mesh=mesh;
302
303 end % }}}
304 function md2 = extract(md,area) % {{{
305 %extract - extract a model according to an Argus contour or flag list
306 %
307 % This routine extracts a submodel from a bigger model with respect to a given contour
308 % md must be followed by the corresponding exp file or flags list
309 % It can either be a domain file (argus type, .exp extension), or an array of element flags.
310 % If user wants every element outside the domain to be
311 % extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
312 % an empty string '' will be considered as an empty domain
313 % a string 'all' will be considered as the entire domain
314 %
315 % Usage:
316 % md2=extract(md,area);
317 %
318 % Examples:
319 % md2=extract(md,'Domain.exp');
320 %
321 % See also: EXTRUDE, COLLAPSE
322
323 %copy model
324 md1=md;
325
326 %some checks
327 if ((nargin~=2) | (nargout~=1)),
328 help extract
329 error('extract error message: bad usage');
330 end
331
332 %get elements that are inside area
333 flag_elem=FlagElements(md1,area);
334 if ~any(flag_elem),
335 error('extracted model is empty');
336 end
337
338 %kick out all elements with 3 dirichlets
339 spc_elem=find(~flag_elem);
340 spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
341 flag=ones(md1.mesh.numberofvertices,1);
342 flag(spc_node)=0;
343 pos=find(sum(flag(md1.mesh.elements),2)==0);
344 flag_elem(pos)=0;
345
346 %extracted elements and nodes lists
347 pos_elem=find(flag_elem);
348 pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
349
350 %keep track of some fields
351 numberofvertices1=md1.mesh.numberofvertices;
352 numberofelements1=md1.mesh.numberofelements;
353 numberofvertices2=length(pos_node);
354 numberofelements2=length(pos_elem);
355 flag_node=zeros(numberofvertices1,1);
356 flag_node(pos_node)=1;
357
358 %Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
359 Pelem=zeros(numberofelements1,1);
360 Pelem(pos_elem)=[1:numberofelements2]';
361 Pnode=zeros(numberofvertices1,1);
362 Pnode(pos_node)=[1:numberofvertices2]';
363
364 %renumber the elements (some nodes won't exist anymore)
365 elements_1=md1.mesh.elements;
366 elements_2=elements_1(pos_elem,:);
367 elements_2(:,1)=Pnode(elements_2(:,1));
368 elements_2(:,2)=Pnode(elements_2(:,2));
369 elements_2(:,3)=Pnode(elements_2(:,3));
370 if isa(md1.mesh,'mesh3dprisms'),
371 elements_2(:,4)=Pnode(elements_2(:,4));
372 elements_2(:,5)=Pnode(elements_2(:,5));
373 elements_2(:,6)=Pnode(elements_2(:,6));
374 end
375
376 %OK, now create the new model!
377
378 %take every field from model
379 md2=md1;
380
381 %automatically modify fields
382
383 %loop over model fields
384 model_fields=fields(md1);
385 for i=1:length(model_fields),
386 %get field
387 field=md1.(model_fields{i});
388 fieldsize=size(field);
389 if isobject(field), %recursive call
390 object_fields=fields(md1.(model_fields{i}));
391 for j=1:length(object_fields),
392 %get field
393 field=md1.(model_fields{i}).(object_fields{j});
394 fieldsize=size(field);
395 %size = number of nodes * n
396 if fieldsize(1)==numberofvertices1
397 md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
398 elseif (fieldsize(1)==numberofvertices1+1)
399 md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
400 %size = number of elements * n
401 elseif fieldsize(1)==numberofelements1
402 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
403 end
404 end
405 else
406 %size = number of nodes * n
407 if fieldsize(1)==numberofvertices1
408 md2.(model_fields{i})=field(pos_node,:);
409 elseif (fieldsize(1)==numberofvertices1+1)
410 md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
411 %size = number of elements * n
412 elseif fieldsize(1)==numberofelements1
413 md2.(model_fields{i})=field(pos_elem,:);
414 end
415 end
416 end
417
418 %modify some specific fields
419
420 %Mesh
421 md2.mesh.numberofelements=numberofelements2;
422 md2.mesh.numberofvertices=numberofvertices2;
423 md2.mesh.elements=elements_2;
424
425 %mesh.uppervertex mesh.lowervertex
426 if isa(md1.mesh,'mesh3dprisms'),
427 md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
428 pos=find(~isnan(md2.mesh.uppervertex));
429 md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
430
431 md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
432 pos=find(~isnan(md2.mesh.lowervertex));
433 md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
434
435 md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
436 pos=find(~isnan(md2.mesh.upperelements));
437 md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
438
439 md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
440 pos=find(~isnan(md2.mesh.lowerelements));
441 md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
442 end
443
444 %Initial 2d mesh
445 if isa(md1.mesh,'mesh3dprisms'),
446 flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
447 pos_elem_2d=find(flag_elem_2d);
448 flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
449 pos_node_2d=find(flag_node_2d);
450
451 md2.mesh.numberofelements2d=length(pos_elem_2d);
452 md2.mesh.numberofvertices2d=length(pos_node_2d);
453 md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
454 md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
455 md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
456 md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
457
458 md2.mesh.x2d=md1.mesh.x(pos_node_2d);
459 md2.mesh.y2d=md1.mesh.y(pos_node_2d);
460 end
461
462 %Edges
463 if(dimension(md.mesh)==2),
464 if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
465 %renumber first two columns
466 pos=find(md2.mesh.edges(:,4)~=-1);
467 md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
468 md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
469 md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
470 md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
471 %remove edges when the 2 vertices are not in the domain.
472 md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
473 %Replace all zeros by -1 in the last two columns
474 pos=find(md2.mesh.edges(:,3)==0);
475 md2.mesh.edges(pos,3)=-1;
476 pos=find(md2.mesh.edges(:,4)==0);
477 md2.mesh.edges(pos,4)=-1;
478 %Invert -1 on the third column with last column (Also invert first two columns!!)
479 pos=find(md2.mesh.edges(:,3)==-1);
480 md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
481 md2.mesh.edges(pos,4)=-1;
482 values=md2.mesh.edges(pos,2);
483 md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
484 md2.mesh.edges(pos,1)=values;
485 %Finally remove edges that do not belong to any element
486 pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
487 md2.mesh.edges(pos,:)=[];
488 end
489 end
490
491 %Penalties
492 if ~isnan(md2.stressbalance.vertex_pairing),
493 for i=1:size(md1.stressbalance.vertex_pairing,1);
494 md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
495 end
496 md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
497 end
498 if ~isnan(md2.masstransport.vertex_pairing),
499 for i=1:size(md1.masstransport.vertex_pairing,1);
500 md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
501 end
502 md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
503 end
504
505 %recreate segments
506 if isa(md1.mesh,'mesh2d'),
507 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
508 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
509 md2.mesh.segments=contourenvelope(md2);
510 md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
511 else
512 %First do the connectivity for the contourenvelope in 2d
513 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
514 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
515 segments=contourenvelope(md2);
516 md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
517 md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
518 %Then do it for 3d as usual
519 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
520 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
521 end
522
523 %Boundary conditions: Dirichlets on new boundary
524 %Catch the elements that have not been extracted
525 orphans_elem=find(~flag_elem);
526 orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
527 %Figure out which node are on the boundary between md2 and md1
528 nodestoflag1=intersect(orphans_node,pos_node);
529 nodestoflag2=Pnode(nodestoflag1);
530 if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
531 if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
532 md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
533 md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
534 else
535 md2.stressbalance.spcvx(nodestoflag2)=NaN;
536 md2.stressbalance.spcvy(nodestoflag2)=NaN;
537 disp(' ')
538 disp('!! extract warning: spc values should be checked !!')
539 disp(' ')
540 end
541 %put 0 for vz
542 md2.stressbalance.spcvz(nodestoflag2)=0;
543 end
544 if ~isnan(md1.thermal.spctemperature),
545 md2.thermal.spctemperature(nodestoflag2,1)=1;
546 end
547
548 %Results fields
549 if isstruct(md1.results),
550 md2.results=struct();
551 solutionfields=fields(md1.results);
552 for i=1:length(solutionfields),
553 if isstruct(md1.results.(solutionfields{i}))
554 %get subfields
555 solutionsubfields=fields(md1.results.(solutionfields{i}));
556 for j=1:length(solutionsubfields),
557 field=md1.results.(solutionfields{i}).(solutionsubfields{j});
558 if length(field)==numberofvertices1,
559 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
560 elseif length(field)==numberofelements1,
561 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
562 else
563 md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
564 end
565 end
566 else
567 field=md1.results.(solutionfields{i});
568 if length(field)==numberofvertices1,
569 md2.results.(solutionfields{i})=field(pos_node);
570 elseif length(field)==numberofelements1,
571 md2.results.(solutionfields{i})=field(pos_elem);
572 else
573 md2.results.(solutionfields{i})=field;
574 end
575 end
576 end
577 end
578
579 %Keep track of pos_node and pos_elem
580 md2.mesh.extractedvertices=pos_node;
581 md2.mesh.extractedelements=pos_elem;
582 end % }}}
583 function md = extrude(md,varargin) % {{{
584 %EXTRUDE - vertically extrude a 2d mesh
585 %
586 % vertically extrude a 2d mesh and create corresponding 3d mesh.
587 % The vertical distribution can:
588 % - follow a polynomial law
589 % - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
590 % - be discribed by a list of coefficients (between 0 and 1)
591 %
592 %
593 % Usage:
594 % md=extrude(md,numlayers,extrusionexponent);
595 % md=extrude(md,numlayers,lowerexponent,upperexponent);
596 % md=extrude(md,listofcoefficients);
597 %
598 % Example:
599 % md=extrude(md,15,1.3);
600 % md=extrude(md,15,1.3,1.2);
601 % md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
602 %
603 % See also: MODELEXTRACT, COLLAPSE
604
605 %some checks on list of arguments
606 if ((nargin>4) | (nargin<2) | (nargout~=1)),
607 help extrude;
608 error('extrude error message');
609 end
610
611 %Extrude the mesh
612 if nargin==2, %list of coefficients
613 clist=varargin{1};
614 if any(clist<0) | any(clist>1),
615 error('extrusioncoefficients must be between 0 and 1');
616 end
617 extrusionlist=sort(unique([clist(:);0;1]));
618 numlayers=length(extrusionlist);
619 elseif nargin==3, %one polynomial law
620 if varargin{2}<=0,
621 help extrude;
622 error('extrusionexponent must be >=0');
623 end
624 numlayers=varargin{1};
625 extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
626 elseif nargin==4, %two polynomial laws
627 numlayers=varargin{1};
628 lowerexp=varargin{2};
629 upperexp=varargin{3};
630
631 if varargin{2}<=0 | varargin{3}<=0,
632 help extrude;
633 error('lower and upper extrusionexponents must be >=0');
634 end
635
636 lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
637 upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
638 extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
639
640 end
641
642 if numlayers<2,
643 error('number of layers should be at least 2');
644 end
645 if strcmp(md.mesh.domaintype(),'3D')
646 error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
647 end
648
649 %Initialize with the 2d mesh
650 mesh2d = md.mesh;
651 md.mesh=mesh3dprisms();
652 md.mesh.x = mesh2d.x;
653 md.mesh.y = mesh2d.y;
654 md.mesh.elements = mesh2d.elements;
655 md.mesh.numberofelements = mesh2d.numberofelements;
656 md.mesh.numberofvertices = mesh2d.numberofvertices;
657
658 md.mesh.lat = mesh2d.lat;
659 md.mesh.long = mesh2d.long;
660 md.mesh.hemisphere = mesh2d.hemisphere;
661
662 md.mesh.vertexonboundary = mesh2d.vertexonboundary;
663 md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
664 md.mesh.elementconnectivity = mesh2d.elementconnectivity;
665 md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
666
667 md.mesh.extractedvertices = mesh2d.extractedvertices;
668 md.mesh.extractedelements = mesh2d.extractedelements;
669
670 x3d=[];
671 y3d=[];
672 z3d=[]; %the lower node is on the bed
673 thickness3d=md.geometry.thickness; %thickness and bed for these nodes
674 bed3d=md.geometry.base;
675
676 %Create the new layers
677 for i=1:numlayers,
678 x3d=[x3d; md.mesh.x];
679 y3d=[y3d; md.mesh.y];
680 %nodes are distributed between bed and surface accordingly to the given exponent
681 z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
682 end
683 number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
684
685 %Extrude elements
686 elements3d=[];
687 for i=1:numlayers-1,
688 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
689 end
690 number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
691
692 %Keep a trace of lower and upper nodes
693 lowervertex=NaN*ones(number_nodes3d,1);
694 uppervertex=NaN*ones(number_nodes3d,1);
695 lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
696 uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
697 md.mesh.lowervertex=lowervertex;
698 md.mesh.uppervertex=uppervertex;
699
700 %same for lower and upper elements
701 lowerelements=NaN*ones(number_el3d,1);
702 upperelements=NaN*ones(number_el3d,1);
703 lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
704 upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
705 md.mesh.lowerelements=lowerelements;
706 md.mesh.upperelements=upperelements;
707
708 %Save old mesh
709 md.mesh.x2d=md.mesh.x;
710 md.mesh.y2d=md.mesh.y;
711 md.mesh.elements2d=md.mesh.elements;
712 md.mesh.numberofelements2d=md.mesh.numberofelements;
713 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
714
715 %Build global 3d mesh
716 md.mesh.elements=elements3d;
717 md.mesh.x=x3d;
718 md.mesh.y=y3d;
719 md.mesh.z=z3d;
720 md.mesh.numberofelements=number_el3d;
721 md.mesh.numberofvertices=number_nodes3d;
722 md.mesh.numberoflayers=numlayers;
723
724 %Ok, now deal with the other fields from the 2d mesh:
725
726 %lat long
727 md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
728 md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
729
730 %drag coefficient is limited to nodes that are on the bedrock.
731 md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1);
732
733 %p and q (same deal, except for element that are on the bedrock: )
734 md.friction.p=project3d(md,'vector',md.friction.p,'type','element');
735 md.friction.q=project3d(md,'vector',md.friction.q,'type','element');
736
737 %observations
738 md.inversion.vx_obs=project3d(md,'vector',md.inversion.vx_obs,'type','node');
739 md.inversion.vy_obs=project3d(md,'vector',md.inversion.vy_obs,'type','node');
740 md.inversion.vel_obs=project3d(md,'vector',md.inversion.vel_obs,'type','node');
741 md.inversion.thickness_obs=project3d(md,'vector',md.inversion.thickness_obs,'type','node');
742 md.surfaceforcings = extrude(md.surfaceforcings,md);
743 md.balancethickness.thickening_rate=project3d(md,'vector',md.balancethickness.thickening_rate,'type','node');
744
745 %results
746 if ~isnan(md.initialization.vx),md.initialization.vx=project3d(md,'vector',md.initialization.vx,'type','node');end;
747 if ~isnan(md.initialization.vy),md.initialization.vy=project3d(md,'vector',md.initialization.vy,'type','node');end;
748 if ~isnan(md.initialization.vz),md.initialization.vz=project3d(md,'vector',md.initialization.vz,'type','node');end;
749 if ~isnan(md.initialization.vel),md.initialization.vel=project3d(md,'vector',md.initialization.vel,'type','node');end;
750 if ~isnan(md.initialization.temperature),md.initialization.temperature=project3d(md,'vector',md.initialization.temperature,'type','node');end;
751 if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project3d(md,'vector',md.initialization.waterfraction,'type','node');end;
752 if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project3d(md,'vector',md.initialization.watercolumn,'type','node','layer',1);end;
753 if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project3d(md,'vector',md.initialization.sediment_head,'type','node','layer',1);end;
754 if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project3d(md,'vector',md.initialization.epl_head,'type','node','layer',1);end;
755 if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project3d(md,'vector',md.initialization.epl_thickness,'type','node','layer',1);end;
756
757 %bedinfo and surface info
758 md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
759 md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
760
761 %elementstype
762 if ~isnan(md.flowequation.element_equation)
763 oldelements_type=md.flowequation.element_equation;
764 md.flowequation.element_equation=zeros(number_el3d,1);
765 md.flowequation.element_equation=project3d(md,'vector',oldelements_type,'type','element');
766 end
767
768 %verticestype
769 if ~isnan(md.flowequation.vertex_equation)
770 oldvertices_type=md.flowequation.vertex_equation;
771 md.flowequation.vertex_equation=zeros(number_nodes3d,1);
772 md.flowequation.vertex_equation=project3d(md,'vector',oldvertices_type,'type','node');
773 end
774 md.flowequation.borderSSA=project3d(md,'vector',md.flowequation.borderSSA,'type','node');
775 md.flowequation.borderHO=project3d(md,'vector',md.flowequation.borderHO,'type','node');
776 md.flowequation.borderFS=project3d(md,'vector',md.flowequation.borderFS,'type','node');
777
778 %boundary conditions
779 md.stressbalance.spcvx=project3d(md,'vector',md.stressbalance.spcvx,'type','node');
780 md.stressbalance.spcvy=project3d(md,'vector',md.stressbalance.spcvy,'type','node');
781 md.stressbalance.spcvz=project3d(md,'vector',md.stressbalance.spcvz,'type','node');
782 md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',NaN);
783 if (length(md.initialization.temperature)==md.mesh.numberofvertices),
784 md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1);
785 if isprop(md.mesh,'vertexonsurface'),
786 pos=find(md.mesh.vertexonsurface);
787 md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface
788 end
789 end
790 md.masstransport.spcthickness=project3d(md,'vector',md.masstransport.spcthickness,'type','node');
791 md.masstransport.calvingrate=project3d(md,'vector',md.masstransport.calvingrate,'type','node');
792 md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
793 md.damage.spcdamage=project3d(md,'vector',md.damage.spcdamage,'type','node');
794 md.stressbalance.referential=project3d(md,'vector',md.stressbalance.referential,'type','node');
795 md.stressbalance.loadingforce=project3d(md,'vector',md.stressbalance.loadingforce,'type','node');
796
797 % Hydrologydc variables
798 if isa(md.hydrology,'hydrologydc');
799 md.hydrology.spcsediment_head=project3d(md,'vector',md.hydrology.spcsediment_head,'type','node','layer',1);
800 md.hydrology.mask_eplactive_node=project3d(md,'vector',md.hydrology.mask_eplactive_node,'type','node','layer',1);
801 md.hydrology.sediment_transmitivity=project3d(md,'vector',md.hydrology.sediment_transmitivity,'type','node','layer',1);
802 md.hydrology.basal_moulin_input=project3d(md,'vector',md.hydrology.basal_moulin_input,'type','node','layer',1);
803 if(md.hydrology.isefficientlayer==1);
804 md.hydrology.spcepl_head=project3d(md,'vector',md.hydrology.spcepl_head,'type','node','layer',1);
805 end
806 end
807
808 %connectivity
809 if ~isnan(md.mesh.elementconnectivity)
810 md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
811 md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
812 for i=2:numlayers-1,
813 md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
814 =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
815 end
816 md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
817 end
818
819 %materials
820 md.materials.rheology_B=project3d(md,'vector',md.materials.rheology_B,'type','node');
821 md.materials.rheology_n=project3d(md,'vector',md.materials.rheology_n,'type','element');
822
823 %damage
824 md.damage.D=project3d(md,'vector',md.damage.D,'type','node');
825
826 %parameters
827 md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
828 md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
829 md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node');
830 md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node');
831 md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
832 md.geometry.base=project3d(md,'vector',md.geometry.base,'type','node');
833 md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
834 md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
835 md.mask.groundedice_levelset=project3d(md,'vector',md.mask.groundedice_levelset,'type','node');
836 md.mask.ice_levelset=project3d(md,'vector',md.mask.ice_levelset,'type','node');
837 if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end;
838 if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end;
839 if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end;
840 if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end
841
842 %Put lithostatic pressure if there is an existing pressure
843 if ~isnan(md.initialization.pressure),
844 md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z);
845 end
846
847 %special for thermal modeling:
848 md.basalforcings.groundedice_melting_rate=project3d(md,'vector',md.basalforcings.groundedice_melting_rate,'type','node','layer',1);
849 md.basalforcings.floatingice_melting_rate=project3d(md,'vector',md.basalforcings.floatingice_melting_rate,'type','node','layer',1);
850 if ~isnan(md.basalforcings.geothermalflux)
851 md.basalforcings.geothermalflux=project3d(md,'vector',md.basalforcings.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux
852 end
853
854 %increase connectivity if less than 25:
855 if md.mesh.average_vertex_connectivity<=25,
856 md.mesh.average_vertex_connectivity=100;
857 end
858 end % }}}
859 function md = structtomodel(md,structmd) % {{{
860
861 if ~isstruct(structmd) error('input model is not a structure'); end
862
863 %loaded model is a struct, initialize output and recover all fields
864 md = structtoobj(model,structmd);
865
866 %Old field now classes
867 if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
868 if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
869
870 %Field name change
871 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
872 if isfield(structmd,'p'), md.friction.p=structmd.p; end
873 if isfield(structmd,'q'), md.friction.q=structmd.p; end
874 if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
875 if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
876 if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
877 if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
878 if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
879 if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
880 if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
881 if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
882 if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
883 if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
884 if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
885 if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
886 if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
887 if isfield(structmd,'g'), md.constants.g=structmd.g; end
888 if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
889 if isfield(structmd,'surface_mass_balance'), md.surfaceforcings.mass_balance=structmd.surface_mass_balance; end
890 if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
891 if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
892 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
893 if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
894 if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
895 if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
896 if isfield(structmd,'riftproperties'), %old implementation
897 md.rifts=rifts();
898 md.rifts.riftproperties=structmd.riftproperties;
899 md.rifts.riftstruct=structmd.rifts;
900 md.rifts.riftproperties=structmd.riftinfo;
901 end
902 if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
903 if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
904 if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
905 if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
906 if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
907 if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
908 if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
909 if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
910 if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
911 if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
912 if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
913 if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
914 if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
915 if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
916 if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
917 if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
918 if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
919 if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
920 if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
921 if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
922 if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
923 if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
924 if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
925 if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
926 if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
927 if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
928 if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
929 if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
930 if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
931 if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
932 if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
933 if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
934 if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
935 if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
936 if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
937 if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
938 if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
939 if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
940 if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
941 if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
942 if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
943 if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
944 if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
945 if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
946 if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
947 if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
948 if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
949 if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
950 if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
951 if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
952 if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
953 if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
954 if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
955 if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
956 if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
957 if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
958 if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
959 if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
960 if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
961 if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
962 if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
963 if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
964 if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
965 if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
966 if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
967 if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
968 if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
969 if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
970 if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
971 if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
972 if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
973 if isfield(structmd,'hemisphere'), md.mesh.hemisphere=structmd.hemisphere; end
974 if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
975 if isfield(structmd,'long'), md.mesh.long=structmd.long; end
976 if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
977 if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
978 if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
979 if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
980 if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
981 if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
982 if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
983 if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
984 if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
985 if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
986 if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
987 if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
988 if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
989 if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
990 if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
991 if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
992 if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
993 if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
994 if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
995 if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
996 if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
997 if isfield(structmd,'edges'),
998 md.mesh.edges=structmd.edges;
999 md.mesh.edges(isnan(md.mesh.edges))=-1;
1000 end
1001 if isfield(structmd,'y'), md.mesh.y=structmd.y; end
1002 if isfield(structmd,'x'), md.mesh.x=structmd.x; end
1003 if isfield(structmd,'z'), md.mesh.z=structmd.z; end
1004 if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
1005 if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
1006 if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
1007 if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
1008
1009 if isnumeric(md.verbose),
1010 md.verbose=verbose;
1011 end
1012
1013 if isfield(structmd,'spcvelocity'),
1014 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
1015 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
1016 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1017 pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
1018 pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
1019 pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
1020 end
1021 if isfield(structmd,'spcvx'),
1022 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
1023 pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
1024 end
1025 if isfield(structmd,'spcvy'),
1026 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
1027 pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
1028 end
1029 if isfield(structmd,'spcvz'),
1030 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1031 pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
1032 end
1033 if isfield(structmd,'pressureload'),
1034 if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
1035 pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
1036 pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
1037 pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
1038 end
1039 end
1040 if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
1041 pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
1042 pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
1043 pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
1044 pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
1045 pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
1046 pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
1047 pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
1048 pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
1049 end
1050 if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
1051 pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
1052 pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
1053 pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
1054 pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
1055 pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
1056 pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
1057 pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
1058 pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
1059 end
1060 if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
1061 if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
1062 if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1063 if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1064 end
1065 if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1066 if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1067 if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
1068 if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1069 end
1070 if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1071 if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1072 if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1073 if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1074 end
1075 if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1076 pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1077 pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1078 pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1079 pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1080 pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1081 pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1082 pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1083 pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1084 pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1085 end
1086
1087 if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1088 md.thermal.stabilization=2;
1089 md.masstransport.stabilization=1;
1090 md.balancethickness.stabilization=1;
1091 end
1092 if isnumeric(md.masstransport.hydrostatic_adjustment)
1093 if md.masstransport.hydrostatic_adjustment==269,
1094 md.masstransport.hydrostatic_adjustment='Incremental';
1095 else
1096 md.masstransport.hydrostatic_adjustment='Absolute';
1097 end
1098 end
1099
1100 %New fields
1101 if ~isfield(structmd,'upperelements');
1102 md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1103 md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1104 end
1105 if ~isfield(structmd,'lowerelements');
1106 md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1107 md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1108 end
1109 if ~isfield(structmd,'diagnostic_ref');
1110 md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1111 end
1112 if ~isfield(structmd,'loadingforce');
1113 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1114 end
1115
1116 %2013 August 9
1117 if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1118 disp('Recovering old prognostic class');
1119 md.masstransport=masstransport(structmd.prognostic);
1120 end
1121 %2013 August 9
1122 if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') || isa(structmd.diagnostic,'stressbalance')),
1123 disp('Recovering old diagnostic class');
1124 md.stressbalance=stressbalance(structmd.diagnostic);
1125 end
1126 end% }}}
1127 function md = setdefaultparameters(md) % {{{
1128
1129 %initialize subclasses
1130 md.mesh = mesh2d();
1131 md.mask = mask();
1132 md.constants = constants();
1133 md.geometry = geometry();
1134 md.initialization = initialization();
1135 md.surfaceforcings = SMB();
1136 md.basalforcings = basalforcings();
1137 md.friction = friction();
1138 md.rifts = rifts();
1139 md.timestepping = timestepping();
1140 md.groundingline = groundingline();
1141 md.materials = matice();
1142 md.damage = damage();
1143 md.flowequation = flowequation();
1144 md.debug = debug();
1145 md.verbose = verbose();
1146 md.settings = settings();
1147 md.toolkits = toolkits();
1148 md.cluster = generic();
1149 md.balancethickness = balancethickness();
1150 md.stressbalance = stressbalance();
1151 md.hydrology = hydrologyshreve();
1152 md.masstransport = masstransport();
1153 md.thermal = thermal();
1154 md.steadystate = steadystate();
1155 md.transient = transient();
1156 md.gia = gia();
1157 md.seaice = seaice();
1158 md.autodiff = autodiff();
1159 md.flaim = flaim();
1160 md.inversion = inversion();
1161 md.qmu = qmu();
1162 md.radaroverlay = radaroverlay();
1163 md.results = struct();
1164 md.outputdefinition = outputdefinition();
1165 md.miscellaneous = miscellaneous();
1166 md.private = private();
1167 end
1168 %}}}
1169 function md = tetras(md,varargin) % {{{
1170 %TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1171 %
1172 % Usage:
1173 % md=tetra(md)
1174
1175 if ~isa(md.mesh,'mesh3dprisms')
1176 error('mesh is not a 3d prismatic mesh');
1177 end
1178
1179 %Initialize tetra mesh
1180 md.mesh=mesh3dtetras(md.mesh);
1181
1182 %Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
1183 steiner = 0;
1184 nbv = md.mesh.numberofvertices;
1185 nbt = 3*md.mesh.numberofelements;
1186 elements = zeros(nbt,4);
1187 for i=1:md.mesh.numberofelements
1188 v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
1189 v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
1190 if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1191 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1192 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1193 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1194 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1195 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1196 elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
1197 elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
1198 elements(end+1,:) = [v2 v3 v5 v7];
1199 elements(end+1,:) = [v3 v5 v6 v7];
1200 elements(end+1,:) = [v1 v3 v6 v7];
1201 elements(end+1,:) = [v1 v4 v6 v7];
1202 elements(end+1,:) = [v4 v5 v6 v7];
1203 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1204 elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
1205 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1206 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1207 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1208 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1209 elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
1210 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1211 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1212 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1213 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1214 elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
1215 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1216 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1217 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1218 elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
1219 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1220 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1221 elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
1222 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1223 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1224 elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
1225 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1226 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1227 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1228 elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
1229 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1230 elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
1231 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1232 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1233 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1234 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1235 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1236 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1237 elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
1238 elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
1239 elements(end+1,:) = [v2 v5 v6 v7];
1240 elements(end+1,:) = [v2 v3 v6 v7];
1241 elements(end+1,:) = [v3 v4 v6 v7];
1242 elements(end+1,:) = [v1 v3 v4 v7];
1243 elements(end+1,:) = [v4 v5 v6 v7];
1244 else
1245 error('Case not supported'); %not supposed to happen!
1246 end
1247 %Reorder elements to make sure they are direct
1248 for j=1:3
1249 element = elements(3*(i-1)+j,:);
1250 matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
1251 if det(matrix)>0,
1252 elements(3*(i-1)+j,1)=element(2);
1253 elements(3*(i-1)+j,2)=element(1);
1254 end
1255 end
1256 end
1257 %%Split in 3 tetras
1258 %subelement1 = [1 2 3 5];
1259 %subelement2 = [4 6 5 1];
1260 %subelement3 = [5 6 3 1];
1261 %elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
1262 if steiner==0,
1263 disp('No Steiner point required to split prismatic mesh into tets');
1264 else
1265 disp([num2str(steiner) ' Steiner points had to be included'])
1266 error('Steiner point not supported yet');
1267 end
1268
1269 pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1270
1271 md.mesh.elements=elements;
1272 md.mesh.numberofelements=size(elements,1);
1273
1274 %p and q (same deal, except for element that are on the bedrock: )
1275 if ~isnan(md.friction.p),
1276 md.friction.p=md.friction.p(pos_elements);
1277 md.friction.q=md.friction.q(pos_elements);
1278 end
1279
1280 %elementstype
1281 if ~isnan(md.flowequation.element_equation)
1282 oldelements_type=md.flowequation.element_equation;
1283 md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1284 end
1285
1286 %connectivity
1287 md.mesh.elementconnectivity=NaN;
1288
1289 %materials
1290 if ~isnan(md.materials.rheology_n),
1291 md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1292 end
1293
1294 %increase connectivity if less than 25:
1295 if md.mesh.average_vertex_connectivity<=25,
1296 md.mesh.average_vertex_connectivity=100;
1297 end
1298 end % }}}
1299 function disp(obj) % {{{
1300 disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(obj.mesh) ']'],'mesh properties'));
1301 disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(obj.mask) ']'],'defines grounded and floating elements'));
1302 disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(obj.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1303 disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(obj.constants) ']'],'physical constants'));
1304 disp(sprintf('%19s: %-22s -- %s','surfaceforcings' ,['[1x1 ' class(obj.surfaceforcings) ']'],'surface forcings'));
1305 disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(obj.basalforcings) ']'],'bed forcings'));
1306 disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(obj.materials) ']'],'material properties'));
1307 disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(obj.damage) ']'],'parameters for damage evolution solution'));
1308 disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(obj.friction) ']'],'basal friction/drag properties'));
1309 disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(obj.flowequation) ']'],'flow equations'));
1310 disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(obj.timestepping) ']'],'time stepping for transient models'));
1311 disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(obj.initialization) ']'],'initial guess/state'));
1312 disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(obj.rifts) ']'],'rifts properties'));
1313 disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(obj.debug) ']'],'debugging tools (valgrind, gprof)'));
1314 disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
1315 disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
1316 disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(obj.toolkits) ']'],'PETSc options for each solution'));
1317 disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
1318 disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
1319 disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(obj.stressbalance) ']'],'parameters for stressbalance solution'));
1320 disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(obj.groundingline) ']'],'parameters for groundingline solution'));
1321 disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(obj.hydrology) ']'],'parameters for hydrology solution'));
1322 disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(obj.masstransport) ']'],'parameters for masstransport solution'));
1323 disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(obj.thermal) ']'],'parameters for thermal solution'));
1324 disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
1325 disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
1326 disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(obj.gia) ']'],'parameters for gia solution'));
1327 disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
1328 disp(sprintf('%19s: %-22s -- %s','flaim' ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
1329 disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(obj.inversion) ']'],'parameters for inverse methods'));
1330 disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(obj.qmu) ']'],'dakota properties'));
1331 disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(obj.outputdefinition) ']'],'output definition'));
1332 disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(obj.results) ']'],'model results'));
1333 disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(obj.radaroverlay) ']'],'radar image for plot overlay'));
1334 disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields'));
1335 disp(sprintf('%19s: %-22s -- %s','seaice' ,['[1x1 ' class(obj.seaice) ']'],'parameters for Sea Ice solution'));
1336 end % }}}
1337 function memory(obj) % {{{
1338
1339 disp(sprintf('\nMemory imprint:\n'));
1340
1341 fields=properties('model');
1342 mem=0;
1343
1344 for i=1:length(fields),
1345 field=obj.(fields{i});
1346 s=whos('field');
1347 mem=mem+s.bytes/1e6;
1348 disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1349 end
1350 disp(sprintf('%19s--%10s','--------------','--------------'));
1351 disp(sprintf('%19s: %g Mb','Total',mem));
1352 end % }}}
1353 function netcdf(obj,filename) % {{{
1354 %NETCDF - save model as netcdf
1355 %
1356 % Usage:
1357 % netcdf(md,filename)
1358 %
1359 % Example:
1360 % netcdf(md,'model.nc');
1361
1362 disp('Saving model as NetCDF');
1363 %1. Create NetCDF file
1364 ncid=netcdf.create(filename,'CLOBBER');
1365 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1366 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' obj.miscellaneous.name ')']);
1367 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1368 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1369
1370 %Preallocate variable id, needed to write variables in netcdf file
1371 var_id=zeros(1000,1);%preallocate
1372
1373 for step=1:2,
1374 counter=0;
1375 [var_id,counter]=structtonc(ncid,'md',obj,0,var_id,counter,step);
1376 if step==1, netcdf.endDef(ncid); end
1377 end
1378
1379 if counter>1000,
1380 warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1381 end
1382
1383 netcdf.close(ncid)
1384 end % }}}
1385 function xylim(obj) % {{{
1386
1387 xlim([min(obj.mesh.x) max(obj.mesh.x)]);
1388 ylim([min(obj.mesh.y) max(obj.mesh.y)])
1389 end % }}}
1390 function md=upload(md) % {{{
1391 %the goal of this routine is to upload the model onto a server, and to empty it.
1392 %So first, save the model with a unique name and upload the file to the server:
1393 random_part=fix(rand(1)*10000);
1394 id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1395 eval(['save ' id ' md']);
1396
1397 %Now, upload the file:
1398 issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1399
1400 %Now, empty this model of everything except settings, and record name of file we just uploaded!
1401 settings_back=md.settings;
1402 md=model();
1403 md.settings=settings_back;
1404 md.settings.upload_filename=id;
1405
1406 %get locally rid of file that was uploaded
1407 eval(['delete ' id]);
1408
1409 end % }}}
1410 function md=download(md) % {{{
1411
1412 %the goal of this routine is to download the internals of the current model from a server, because
1413 %this model is empty, except for the settings which tell us where to go and find this model!
1414
1415 %Download the file:
1416 issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1417
1418 name=md.settings.upload_filename;
1419
1420 %Now, load this model:
1421 md=loadmodel(md.settings.upload_filename);
1422
1423 %get locally rid of file that was downloaded
1424 eval(['delete ' name]);
1425
1426 end % }}}
1427 end
1428 end
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