source: issm/trunk-jpl/src/m/classes/model.m@ 21544

Last change on this file since 21544 was 21544, checked in by Mathieu Morlighem, 9 years ago

BUG: keep old gia class
File size: 64.7 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 giaivins = 0;
43 esa = 0;
44
45 autodiff = 0;
46 inversion = 0;
47 qmu = 0;
48
49 results = 0;
50 outputdefinition = 0;
51 radaroverlay = 0;
52 miscellaneous = 0;
53 private = 0;
54
55 %}}}
56 end
57 methods (Static)
58 function md = loadobj(md) % {{{
59 % This function is directly called by matlab when a model object is
60 % loaded. If the input is a struct it is an old version of model and
61 % old fields must be recovered (make sure they are in the deprecated
62 % model properties)
63
64 if verLessThan('matlab','7.9'),
65 disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
66 disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
67
68 % This is a Matlab bug: all the fields of md have their default value
69 % Example of error message:
70 % Warning: Error loading an object of class 'model':
71 % Undefined function or method 'exist' for input arguments of type 'cell'
72 %
73 % This has been fixed in MATLAB 7.9 (R2009b) and later versions
74 end
75
76 if isstruct(md)
77 disp('Recovering model object from a previous version');
78 md = structtomodel(model,md);
79 end
80
81 %2012 August 4th
82 if isa(md.materials,'materials'),
83 disp('Recovering old materials');
84 if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
85 md.materials=matice(md.materials);
86 else
87 md.materials=matdamageice(md.materials);
88 end
89 end
90 %2013 April 12
91 if numel(md.stressbalance.loadingforce==1)
92 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
93 end
94 %2013 April 17
95 if isa(md.hydrology,'hydrology'),
96 disp('Recovering old hydrology class');
97 md.hydrology=hydrologyshreve(md.materials);
98 end
99 %2013 October 9
100 if ~isa(md.damage,'damage'),
101 md.damage=damage();
102 md.damage.D=zeros(md.mesh.numberofvertices,1);
103 md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
104 end
105 %2013 November 18
106 if ~isa(md.outputdefinition,'outputdefinition'),
107 md.outputdefinition=outputdefinition();
108 end
109 %2014 March 26th
110 if isa(md.mesh,'mesh'),
111 disp('Recovering old mesh class');
112 if isprop(md.mesh,'dimension'),
113 if md.mesh.dimension==2,
114 md.mesh=mesh2d(md.mesh);
115 else
116 md.mesh=mesh3dprisms(md.mesh);
117 end
118 else
119 md.mesh=mesh2dvertical(md.mesh);
120 end
121 end
122 %2014 November 12
123 if isa(md.calving,'double');
124 md.calving=calving();
125 end
126 %2016 February 3
127 if isa(md.slr,'double');
128 md.slr=slr();
129 end
130 %2016 October 11
131 if isa(md.esa,'double');
132 md.esa=esa();
133 end
134
135 end% }}}
136 end
137 methods
138 function md = model(varargin) % {{{
139
140 switch nargin
141 case 0
142 md=setdefaultparameters(md);
143 case 1
144 error('model constructor not supported yet');
145
146 otherwise
147 error('model constructor error message: 0 of 1 argument only in input.');
148 end
149 end
150 %}}}
151 function md = checkmessage(md,string) % {{{
152 if(nargout~=1) error('wrong usage, model must be an output'); end
153 disp(['model not consistent: ' string]);
154 md.private.isconsistent=false;
155 end
156 %}}}
157 function md = collapse(md)% {{{
158 %COLLAPSE - collapses a 3d mesh into a 2d mesh
159 %
160 % This routine collapses a 3d model into a 2d model
161 % and collapses all the fileds of the 3d model by
162 % taking their depth-averaged values
163 %
164 % Usage:
165 % md=collapse(md)
166 %
167 % See also: EXTRUDE, MODELEXTRACT
168
169 %Check that the model is really a 3d model
170 if ~strcmp(md.mesh.elementtype(),'Penta'),
171 error('collapse error message: only 3d mesh can be collapsed')
172 end
173
174 %Start with changing all the fields from the 3d mesh
175
176 %dealing with the friciton law
177 %drag is limited to nodes that are on the bedrock.
178 if isa(md.friction,'friction'),
179 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
180 md.friction.p=project2d(md,md.friction.p,1);
181 md.friction.q=project2d(md,md.friction.q,1);
182 elseif isa(md.friction,'frictionhydro'),
183 md.friction.q=project2d(md,md.friction.q,1);
184 md.friction.C=project2d(md,md.friction.C,1);
185 md.friction.As=project2d(md,md.friction.As,1);
186 md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
187 elseif isa(md.friction,'frictionwaterlayer'),
188 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
189 md.friction.p=project2d(md,md.friction.p,1);
190 md.friction.q=project2d(md,md.friction.q,1);
191 md.friction.water_layer=project2d(md,md.friction.water_layer,1);
192 elseif isa(md.friction,'frictionweertman'),
193 md.friction.C=project2d(md,md.friction.C,1);
194 md.friction.m=project2d(md,md.friction.m,1);
195 elseif isa(md.friction,'frictionweertmantemp'),
196 md.friction.C=project2d(md,md.friction.C,1);
197 md.friction.m=project2d(md,md.friction.m,1);
198 else
199 disp('friction type not supported');
200 end
201
202 %observations
203 if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
204 if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
205 if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
206 if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
207 if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
208 if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
209 if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
210 md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
211 elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
212 md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
213 end;
214
215 %results
216 if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
217 if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
218 if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
219 if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
220 if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
221 if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
222 if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
223 if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
224 if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
225 if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
226 if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
227 %giaivins
228 if ~isnan(md.giaivins.mantle_viscosity), md.giaivins.mantle_viscosity=project2d(md,md.giaivins.mantle_viscosity,1); end
229 if ~isnan(md.giaivins.lithosphere_thickness), md.giaivins.lithosphere_thickness=project2d(md,md.giaivins.lithosphere_thickness,1); end
230
231 %elementstype
232 if ~isnan(md.flowequation.element_equation)
233 md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
234 md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
235 md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
236 md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
237 md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
238 end
239
240 %boundary conditions
241 md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
242 md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
243 md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
244 md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
245 md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
246 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
247 if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
248 if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
249 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
250
251 % Hydrologydc variables
252 if isa(md.hydrology,'hydrologydc');
253 md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
254 md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
255 md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
256 md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
257 if(md.hydrology.isefficientlayer==1)
258 md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
259 end
260 end
261
262 %materials
263 md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
264 md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
265
266 %damage:
267 if md.damage.isdamage,
268 md.damage.D=DepthAverage(md,md.damage.D);
269 end
270
271 %special for thermal modeling:
272 if ~isnan(md.basalforcings.groundedice_melting_rate),
273 md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
274 end
275 if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
276 md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
277 end
278 md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
279
280 if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
281 md.calving.coeff=project2d(md,md.calving.coeff,1);
282 end
283 if isprop(md.calving,'meltingrate') & ~isnan(md.calving.meltingrate),
284 md.calving.meltingrate=project2d(md,md.calving.meltingrate,1);
285 end
286
287 %update of connectivity matrix
288 md.mesh.average_vertex_connectivity=25;
289
290 %Collapse the mesh
291 nodes2d=md.mesh.numberofvertices2d;
292 elements2d=md.mesh.numberofelements2d;
293
294 %parameters
295 md.geometry.surface=project2d(md,md.geometry.surface,1);
296 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
297 md.geometry.base=project2d(md,md.geometry.base,1);
298 if ~isnan(md.geometry.bed),
299 md.geometry.bed=project2d(md,md.geometry.bed,1);
300 end
301
302 if ~isnan(md.mask.groundedice_levelset),
303 md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
304 end
305 if ~isnan(md.mask.ice_levelset),
306 md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
307 end
308
309 %Initialize with the 2d mesh
310 mesh=mesh2d();
311 mesh.x=md.mesh.x2d;
312 mesh.y=md.mesh.y2d;
313 mesh.numberofvertices=md.mesh.numberofvertices2d;
314 mesh.numberofelements=md.mesh.numberofelements2d;
315 mesh.elements=md.mesh.elements2d;
316 if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end
317 if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end
318 mesh.epsg=md.mesh.epsg;
319 if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
320 if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
321 md.mesh=mesh;
322 md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
323 md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
324 md.mesh.segments=contourenvelope(md.mesh);
325
326 end % }}}
327 function md2 = extract(md,area) % {{{
328 %extract - extract a model according to an Argus contour or flag list
329 %
330 % This routine extracts a submodel from a bigger model with respect to a given contour
331 % md must be followed by the corresponding exp file or flags list
332 % It can either be a domain file (argus type, .exp extension), or an array of element flags.
333 % If user wants every element outside the domain to be
334 % extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
335 % an empty string '' will be considered as an empty domain
336 % a string 'all' will be considered as the entire domain
337 %
338 % Usage:
339 % md2=extract(md,area);
340 %
341 % Examples:
342 % md2=extract(md,'Domain.exp');
343 %
344 % See also: EXTRUDE, COLLAPSE
345
346 %copy model
347 md1=md;
348
349 %some checks
350 if ((nargin~=2) | (nargout~=1)),
351 help extract
352 error('extract error message: bad usage');
353 end
354
355 %get elements that are inside area
356 flag_elem=FlagElements(md1,area);
357 if ~any(flag_elem),
358 error('extracted model is empty');
359 end
360
361 %kick out all elements with 3 dirichlets
362 spc_elem=find(~flag_elem);
363 spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
364 flag=ones(md1.mesh.numberofvertices,1);
365 flag(spc_node)=0;
366 pos=find(sum(flag(md1.mesh.elements),2)==0);
367 flag_elem(pos)=0;
368
369 %extracted elements and nodes lists
370 pos_elem=find(flag_elem);
371 pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
372
373 %keep track of some fields
374 numberofvertices1=md1.mesh.numberofvertices;
375 numberofelements1=md1.mesh.numberofelements;
376 numberofvertices2=length(pos_node);
377 numberofelements2=length(pos_elem);
378 flag_node=zeros(numberofvertices1,1);
379 flag_node(pos_node)=1;
380
381 %Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
382 Pelem=zeros(numberofelements1,1);
383 Pelem(pos_elem)=[1:numberofelements2]';
384 Pnode=zeros(numberofvertices1,1);
385 Pnode(pos_node)=[1:numberofvertices2]';
386
387 %renumber the elements (some nodes won't exist anymore)
388 elements_1=md1.mesh.elements;
389 elements_2=elements_1(pos_elem,:);
390 elements_2(:,1)=Pnode(elements_2(:,1));
391 elements_2(:,2)=Pnode(elements_2(:,2));
392 elements_2(:,3)=Pnode(elements_2(:,3));
393 if isa(md1.mesh,'mesh3dprisms'),
394 elements_2(:,4)=Pnode(elements_2(:,4));
395 elements_2(:,5)=Pnode(elements_2(:,5));
396 elements_2(:,6)=Pnode(elements_2(:,6));
397 end
398
399 %OK, now create the new model!
400
401 %take every field from model
402 md2=md1;
403
404 %automatically modify fields
405
406 %loop over model fields
407 model_fields=fields(md1);
408 for i=1:length(model_fields),
409 %get field
410 field=md1.(model_fields{i});
411 fieldsize=size(field);
412 if isobject(field), %recursive call
413 object_fields=fields(md1.(model_fields{i}));
414 for j=1:length(object_fields),
415 %get field
416 field=md1.(model_fields{i}).(object_fields{j});
417 fieldsize=size(field);
418 %size = number of nodes * n
419 if fieldsize(1)==numberofvertices1
420 md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
421 elseif (fieldsize(1)==numberofvertices1+1)
422 md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
423 %size = number of elements * n
424 elseif fieldsize(1)==numberofelements1
425 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
426 elseif (fieldsize(1)==numberofelements1+1)
427 md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
428 end
429 end
430 else
431 %size = number of nodes * n
432 if fieldsize(1)==numberofvertices1
433 md2.(model_fields{i})=field(pos_node,:);
434 elseif (fieldsize(1)==numberofvertices1+1)
435 md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
436 %size = number of elements * n
437 elseif fieldsize(1)==numberofelements1
438 md2.(model_fields{i})=field(pos_elem,:);
439 elseif (fieldsize(1)==numberofelements1+1)
440 md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
441 end
442 end
443 end
444
445 %modify some specific fields
446
447 %Mesh
448 md2.mesh.numberofelements=numberofelements2;
449 md2.mesh.numberofvertices=numberofvertices2;
450 md2.mesh.elements=elements_2;
451
452 %mesh.uppervertex mesh.lowervertex
453 if isa(md1.mesh,'mesh3dprisms'),
454 md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
455 pos=find(~isnan(md2.mesh.uppervertex));
456 md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
457
458 md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
459 pos=find(~isnan(md2.mesh.lowervertex));
460 md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
461
462 md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
463 pos=find(~isnan(md2.mesh.upperelements));
464 md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
465
466 md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
467 pos=find(~isnan(md2.mesh.lowerelements));
468 md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
469 end
470
471 %Initial 2d mesh
472 if isa(md1.mesh,'mesh3dprisms'),
473 flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
474 pos_elem_2d=find(flag_elem_2d);
475 flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
476 pos_node_2d=find(flag_node_2d);
477
478 md2.mesh.numberofelements2d=length(pos_elem_2d);
479 md2.mesh.numberofvertices2d=length(pos_node_2d);
480 md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
481 md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
482 md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
483 md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
484
485 md2.mesh.x2d=md1.mesh.x(pos_node_2d);
486 md2.mesh.y2d=md1.mesh.y(pos_node_2d);
487 end
488
489 %Edges
490 if(dimension(md.mesh)==2),
491 if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
492 %renumber first two columns
493 pos=find(md2.mesh.edges(:,4)~=-1);
494 md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
495 md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
496 md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
497 md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
498 %remove edges when the 2 vertices are not in the domain.
499 md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
500 %Replace all zeros by -1 in the last two columns
501 pos=find(md2.mesh.edges(:,3)==0);
502 md2.mesh.edges(pos,3)=-1;
503 pos=find(md2.mesh.edges(:,4)==0);
504 md2.mesh.edges(pos,4)=-1;
505 %Invert -1 on the third column with last column (Also invert first two columns!!)
506 pos=find(md2.mesh.edges(:,3)==-1);
507 md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
508 md2.mesh.edges(pos,4)=-1;
509 values=md2.mesh.edges(pos,2);
510 md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
511 md2.mesh.edges(pos,1)=values;
512 %Finally remove edges that do not belong to any element
513 pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
514 md2.mesh.edges(pos,:)=[];
515 end
516 end
517
518 %Penalties
519 if ~isnan(md2.stressbalance.vertex_pairing),
520 for i=1:size(md1.stressbalance.vertex_pairing,1);
521 md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
522 end
523 md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
524 end
525 if ~isnan(md2.masstransport.vertex_pairing),
526 for i=1:size(md1.masstransport.vertex_pairing,1);
527 md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
528 end
529 md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
530 end
531
532 %recreate segments
533 if isa(md1.mesh,'mesh2d') | isa(md1.mesh','mesh3dsurface'),
534 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
535 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
536 md2.mesh.segments=contourenvelope(md2.mesh);
537 md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
538 else
539 %First do the connectivity for the contourenvelope in 2d
540 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
541 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
542 segments=contourenvelope(md2.mesh);
543 md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
544 md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
545 %Then do it for 3d as usual
546 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
547 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
548 end
549
550 %Boundary conditions: Dirichlets on new boundary
551 %Catch the elements that have not been extracted
552 orphans_elem=find(~flag_elem);
553 orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
554 %Figure out which node are on the boundary between md2 and md1
555 nodestoflag1=intersect(orphans_node,pos_node);
556 nodestoflag2=Pnode(nodestoflag1);
557 if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
558 if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
559 md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
560 md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
561 else
562 md2.stressbalance.spcvx(nodestoflag2)=NaN;
563 md2.stressbalance.spcvy(nodestoflag2)=NaN;
564 disp(' ')
565 disp('!! extract warning: spc values should be checked !!')
566 disp(' ')
567 end
568 %put 0 for vz
569 md2.stressbalance.spcvz(nodestoflag2)=0;
570 end
571 if ~isnan(md1.thermal.spctemperature),
572 md2.thermal.spctemperature(nodestoflag2,1)=1;
573 end
574
575 %Results fields
576 if isstruct(md1.results),
577 md2.results=struct();
578 solutionfields=fields(md1.results);
579 for i=1:length(solutionfields),
580 if isstruct(md1.results.(solutionfields{i}))
581 %get subfields
582 solutionsubfields=fields(md1.results.(solutionfields{i}));
583 for j=1:length(solutionsubfields),
584 field=md1.results.(solutionfields{i}).(solutionsubfields{j});
585 if length(field)==numberofvertices1,
586 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
587 elseif length(field)==numberofelements1,
588 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
589 else
590 md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
591 end
592 end
593 else
594 field=md1.results.(solutionfields{i});
595 if length(field)==numberofvertices1,
596 md2.results.(solutionfields{i})=field(pos_node);
597 elseif length(field)==numberofelements1,
598 md2.results.(solutionfields{i})=field(pos_elem);
599 else
600 md2.results.(solutionfields{i})=field;
601 end
602 end
603 end
604 end
605
606 %Keep track of pos_node and pos_elem
607 md2.mesh.extractedvertices=pos_node;
608 md2.mesh.extractedelements=pos_elem;
609 end % }}}
610 function md = extrude(md,varargin) % {{{
611 %EXTRUDE - vertically extrude a 2d mesh
612 %
613 % vertically extrude a 2d mesh and create corresponding 3d mesh.
614 % The vertical distribution can:
615 % - follow a polynomial law
616 % - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
617 % - be discribed by a list of coefficients (between 0 and 1)
618 %
619 %
620 % Usage:
621 % md=extrude(md,numlayers,extrusionexponent);
622 % md=extrude(md,numlayers,lowerexponent,upperexponent);
623 % md=extrude(md,listofcoefficients);
624 %
625 % Example:
626 % md=extrude(md,15,1.3);
627 % md=extrude(md,15,1.3,1.2);
628 % md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
629 %
630 % See also: MODELEXTRACT, COLLAPSE
631
632 %some checks on list of arguments
633 if ((nargin>4) | (nargin<2) | (nargout~=1)),
634 help extrude;
635 error('extrude error message');
636 end
637
638 %Extrude the mesh
639 if nargin==2, %list of coefficients
640 clist=varargin{1};
641 if any(clist<0) | any(clist>1),
642 error('extrusioncoefficients must be between 0 and 1');
643 end
644 extrusionlist=sort(unique([clist(:);0;1]));
645 numlayers=length(extrusionlist);
646 elseif nargin==3, %one polynomial law
647 if varargin{2}<=0,
648 help extrude;
649 error('extrusionexponent must be >=0');
650 end
651 numlayers=varargin{1};
652 extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
653 elseif nargin==4, %two polynomial laws
654 numlayers=varargin{1};
655 lowerexp=varargin{2};
656 upperexp=varargin{3};
657
658 if varargin{2}<=0 | varargin{3}<=0,
659 help extrude;
660 error('lower and upper extrusionexponents must be >=0');
661 end
662
663 lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
664 upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
665 extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
666
667 end
668
669 if numlayers<2,
670 error('number of layers should be at least 2');
671 end
672 if strcmp(md.mesh.domaintype(),'3D')
673 error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
674 end
675
676 %Initialize with the 2d mesh
677 mesh2d = md.mesh;
678 md.mesh=mesh3dprisms();
679 md.mesh.x = mesh2d.x;
680 md.mesh.y = mesh2d.y;
681 md.mesh.elements = mesh2d.elements;
682 md.mesh.numberofelements = mesh2d.numberofelements;
683 md.mesh.numberofvertices = mesh2d.numberofvertices;
684
685 md.mesh.lat = mesh2d.lat;
686 md.mesh.long = mesh2d.long;
687 md.mesh.epsg = mesh2d.epsg;
688
689 md.mesh.vertexonboundary = mesh2d.vertexonboundary;
690 md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
691 md.mesh.elementconnectivity = mesh2d.elementconnectivity;
692 md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
693
694 md.mesh.extractedvertices = mesh2d.extractedvertices;
695 md.mesh.extractedelements = mesh2d.extractedelements;
696
697 x3d=[];
698 y3d=[];
699 z3d=[]; %the lower node is on the bed
700 thickness3d=md.geometry.thickness; %thickness and bed for these nodes
701 bed3d=md.geometry.base;
702
703 %Create the new layers
704 for i=1:numlayers,
705 x3d=[x3d; md.mesh.x];
706 y3d=[y3d; md.mesh.y];
707 %nodes are distributed between bed and surface accordingly to the given exponent
708 z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
709 end
710 number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
711
712 %Extrude elements
713 elements3d=[];
714 for i=1:numlayers-1,
715 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
716 end
717 number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
718
719 %Keep a trace of lower and upper nodes
720 lowervertex=NaN*ones(number_nodes3d,1);
721 uppervertex=NaN*ones(number_nodes3d,1);
722 lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
723 uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
724 md.mesh.lowervertex=lowervertex;
725 md.mesh.uppervertex=uppervertex;
726
727 %same for lower and upper elements
728 lowerelements=NaN*ones(number_el3d,1);
729 upperelements=NaN*ones(number_el3d,1);
730 lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
731 upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
732 md.mesh.lowerelements=lowerelements;
733 md.mesh.upperelements=upperelements;
734
735 %Save old mesh
736 md.mesh.x2d=md.mesh.x;
737 md.mesh.y2d=md.mesh.y;
738 md.mesh.elements2d=md.mesh.elements;
739 md.mesh.numberofelements2d=md.mesh.numberofelements;
740 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
741
742 %Build global 3d mesh
743 md.mesh.elements=elements3d;
744 md.mesh.x=x3d;
745 md.mesh.y=y3d;
746 md.mesh.z=z3d;
747 md.mesh.numberofelements=number_el3d;
748 md.mesh.numberofvertices=number_nodes3d;
749 md.mesh.numberoflayers=numlayers;
750
751 %Ok, now deal with the other fields from the 2d mesh:
752
753 %bedinfo and surface info
754 md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
755 md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
756 md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
757
758 %lat long
759 md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
760 md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
761
762 md.geometry=extrude(md.geometry,md);
763 md.friction = extrude(md.friction,md);
764 md.inversion = extrude(md.inversion,md);
765 md.smb = extrude(md.smb,md);
766 md.initialization = extrude(md.initialization,md);
767
768 md.flowequation=md.flowequation.extrude(md);
769 md.stressbalance=extrude(md.stressbalance,md);
770 md.thermal=md.thermal.extrude(md);
771 md.masstransport=md.masstransport.extrude(md);
772 md.levelset=extrude(md.levelset,md);
773 md.calving=extrude(md.calving,md);
774 md.hydrology = extrude(md.hydrology,md);
775
776 %connectivity
777 if ~isnan(md.mesh.elementconnectivity)
778 md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
779 md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
780 for i=2:numlayers-1,
781 md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
782 =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
783 end
784 md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
785 end
786
787 md.materials=extrude(md.materials,md);
788 md.damage=extrude(md.damage,md);
789 md.mask=extrude(md.mask,md);
790 md.qmu=extrude(md.qmu,md);
791 md.basalforcings=extrude(md.basalforcings,md);
792
793 %increase connectivity if less than 25:
794 if md.mesh.average_vertex_connectivity<=25,
795 md.mesh.average_vertex_connectivity=100;
796 end
797 end % }}}
798 function md = structtomodel(md,structmd) % {{{
799
800 if ~isstruct(structmd) error('input model is not a structure'); end
801
802 %loaded model is a struct, initialize output and recover all fields
803 md = structtoobj(model,structmd);
804
805 %Old field now classes
806 if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
807 if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
808
809 %Field name change
810 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
811 if isfield(structmd,'p'), md.friction.p=structmd.p; end
812 if isfield(structmd,'q'), md.friction.q=structmd.p; end
813 if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
814 if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
815 if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
816 if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
817 if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
818 if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
819 if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
820 if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
821 if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
822 if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
823 if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
824 if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
825 if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
826 if isfield(structmd,'g'), md.constants.g=structmd.g; end
827 if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
828 if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
829 if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
830 if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
831 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
832 if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
833 if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
834 if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
835 if isfield(structmd,'riftproperties'), %old implementation
836 md.rifts=rifts();
837 md.rifts.riftproperties=structmd.riftproperties;
838 md.rifts.riftstruct=structmd.rifts;
839 md.rifts.riftproperties=structmd.riftinfo;
840 end
841 if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
842 if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
843 if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
844 if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
845 if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
846 if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
847 if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
848 if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
849 if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
850 if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
851 if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
852 if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
853 if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
854 if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
855 if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
856 if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
857 if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
858 if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
859 if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
860 if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
861 if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
862 if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
863 if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
864 if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
865 if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
866 if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
867 if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
868 if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
869 if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
870 if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
871 if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
872 if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
873 if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
874 if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
875 if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
876 if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
877 if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
878 if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
879 if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
880 if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
881 if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
882 if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
883 if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
884 if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
885 if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
886 if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
887 if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
888 if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
889 if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
890 if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
891 if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
892 if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
893 if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
894 if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
895 if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
896 if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
897 if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
898 if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
899 if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
900 if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
901 if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
902 if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
903 if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
904 if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
905 if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
906 if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
907 if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
908 if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
909 if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
910 if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
911 if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
912 if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
913 if isfield(structmd,'long'), md.mesh.long=structmd.long; end
914 if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
915 if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
916 if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
917 if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
918 if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
919 if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
920 if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
921 if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
922 if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
923 if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
924 if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
925 if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
926 if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
927 if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
928 if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
929 if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
930 if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
931 if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
932 if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
933 if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
934 if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
935 if isfield(structmd,'edges'),
936 md.mesh.edges=structmd.edges;
937 md.mesh.edges(isnan(md.mesh.edges))=-1;
938 end
939 if isfield(structmd,'y'), md.mesh.y=structmd.y; end
940 if isfield(structmd,'x'), md.mesh.x=structmd.x; end
941 if isfield(structmd,'z'), md.mesh.z=structmd.z; end
942 if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
943 if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
944 if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
945
946 if isnumeric(md.verbose),
947 md.verbose=verbose;
948 end
949
950 if isfield(structmd,'spcvelocity'),
951 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
952 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
953 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
954 pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
955 pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
956 pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
957 end
958 if isfield(structmd,'spcvx'),
959 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
960 pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
961 end
962 if isfield(structmd,'spcvy'),
963 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
964 pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
965 end
966 if isfield(structmd,'spcvz'),
967 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
968 pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
969 end
970 if isfield(structmd,'pressureload'),
971 if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
972 pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
973 pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
974 pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
975 end
976 end
977 if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
978 pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
979 pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
980 pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
981 pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
982 pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
983 pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
984 pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
985 pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
986 end
987 if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
988 pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
989 pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
990 pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
991 pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
992 pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
993 pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
994 pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
995 pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
996 end
997 if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
998 if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
999 if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1000 if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1001 end
1002 if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1003 if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1004 if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
1005 if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1006 end
1007 if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1008 if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1009 if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1010 if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1011 end
1012 if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1013 pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1014 pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1015 pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1016 pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1017 pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1018 pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1019 pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1020 pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1021 pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1022 end
1023
1024 if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1025 md.thermal.stabilization=2;
1026 md.masstransport.stabilization=1;
1027 md.balancethickness.stabilization=1;
1028 end
1029 if isnumeric(md.masstransport.hydrostatic_adjustment)
1030 if md.masstransport.hydrostatic_adjustment==269,
1031 md.masstransport.hydrostatic_adjustment='Incremental';
1032 else
1033 md.masstransport.hydrostatic_adjustment='Absolute';
1034 end
1035 end
1036
1037 %New fields
1038 if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
1039 md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1040 md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1041 end
1042 if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
1043 md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1044 md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1045 end
1046 if ~isfield(structmd,'diagnostic_ref');
1047 md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1048 end
1049 if ~isfield(structmd,'loadingforce');
1050 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1051 end
1052
1053 %2013 August 9
1054 if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1055 disp('Recovering old prognostic class');
1056 md.masstransport=masstransport(structmd.prognostic);
1057 end
1058 %2013 August 9
1059 if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') || isa(structmd.diagnostic,'stressbalance')),
1060 disp('Recovering old diagnostic class');
1061 md.stressbalance=stressbalance(structmd.diagnostic);
1062 end
1063 %2014 January 9th
1064 if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
1065 disp('Recovering old surfaceforcings class');
1066 mass_balance=structmd.surfaceforcings.mass_balance;
1067 md.smb=SMB();
1068 md.smb.mass_balance=mass_balance;
1069 end
1070 %2015 September 10
1071 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
1072 disp('Recovering old SMB class');
1073 md.smb=SMBforcing(structmd.surfaceforcings);
1074 end
1075 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
1076 disp('Recovering old SMBhenning class');
1077 md.smb=SMBhenning(structmd.surfaceforcings);
1078 end
1079
1080 end% }}}
1081 function md = setdefaultparameters(md) % {{{
1082
1083 %initialize subclasses
1084 md.mesh = mesh2d();
1085 md.mask = mask();
1086 md.constants = constants();
1087 md.geometry = geometry();
1088 md.initialization = initialization();
1089 md.smb = SMBforcing();
1090 md.basalforcings = basalforcings();
1091 md.friction = friction();
1092 md.rifts = rifts();
1093 md.slr = slr();
1094 md.timestepping = timestepping();
1095 md.groundingline = groundingline();
1096 md.materials = matice();
1097 md.damage = damage();
1098 md.flowequation = flowequation();
1099 md.debug = debug();
1100 md.verbose = verbose();
1101 md.settings = settings();
1102 md.toolkits = toolkits();
1103 md.cluster = generic();
1104 md.balancethickness = balancethickness();
1105 md.stressbalance = stressbalance();
1106 md.hydrology = hydrologyshreve();
1107 md.masstransport = masstransport();
1108 md.thermal = thermal();
1109 md.steadystate = steadystate();
1110 md.transient = transient();
1111 md.levelset = levelset();
1112 md.calving = calving();
1113 md.giaivins = giaivins();
1114 md.esa = esa();
1115 md.autodiff = autodiff();
1116 md.inversion = inversion();
1117 md.qmu = qmu();
1118 md.radaroverlay = radaroverlay();
1119 md.results = struct();
1120 md.outputdefinition = outputdefinition();
1121 md.miscellaneous = miscellaneous();
1122 md.private = private();
1123 end
1124 %}}}
1125 function md = tetras(md,varargin) % {{{
1126 %TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1127 %
1128 % Usage:
1129 % md=tetra(md)
1130
1131 if ~isa(md.mesh,'mesh3dprisms')
1132 error('mesh is not a 3d prismatic mesh');
1133 end
1134
1135 %Initialize tetra mesh
1136 md.mesh=mesh3dtetras(md.mesh);
1137
1138 %Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
1139 steiner = 0;
1140 nbv = md.mesh.numberofvertices;
1141 nbt = 3*md.mesh.numberofelements;
1142 elements = zeros(nbt,4);
1143 for i=1:md.mesh.numberofelements
1144 v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
1145 v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
1146 if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1147 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1148 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1149 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1150 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1151 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1152 elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
1153 elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
1154 elements(end+1,:) = [v2 v3 v5 v7];
1155 elements(end+1,:) = [v3 v5 v6 v7];
1156 elements(end+1,:) = [v1 v3 v6 v7];
1157 elements(end+1,:) = [v1 v4 v6 v7];
1158 elements(end+1,:) = [v4 v5 v6 v7];
1159 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1160 elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
1161 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1162 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1163 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1164 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1165 elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
1166 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1167 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1168 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1169 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1170 elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
1171 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1172 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1173 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1174 elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
1175 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1176 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1177 elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
1178 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1179 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1180 elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
1181 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1182 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1183 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1184 elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
1185 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1186 elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
1187 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1188 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1189 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1190 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1191 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1192 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1193 elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
1194 elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
1195 elements(end+1,:) = [v2 v5 v6 v7];
1196 elements(end+1,:) = [v2 v3 v6 v7];
1197 elements(end+1,:) = [v3 v4 v6 v7];
1198 elements(end+1,:) = [v1 v3 v4 v7];
1199 elements(end+1,:) = [v4 v5 v6 v7];
1200 else
1201 error('Case not supported'); %not supposed to happen!
1202 end
1203 %Reorder elements to make sure they are direct
1204 for j=1:3
1205 element = elements(3*(i-1)+j,:);
1206 matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
1207 if det(matrix)>0,
1208 elements(3*(i-1)+j,1)=element(2);
1209 elements(3*(i-1)+j,2)=element(1);
1210 end
1211 end
1212 end
1213 %%Split in 3 tetras
1214 %subelement1 = [1 2 3 5];
1215 %subelement2 = [4 6 5 1];
1216 %subelement3 = [5 6 3 1];
1217 %elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
1218 if steiner==0,
1219 disp('No Steiner point required to split prismatic mesh into tets');
1220 else
1221 disp([num2str(steiner) ' Steiner points had to be included'])
1222 error('Steiner point not supported yet');
1223 end
1224
1225 pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1226
1227 md.mesh.elements=elements;
1228 md.mesh.numberofelements=size(elements,1);
1229
1230 %p and q (same deal, except for element that are on the bedrock: )
1231 if ~isnan(md.friction.p),
1232 md.friction.p=md.friction.p(pos_elements);
1233 md.friction.q=md.friction.q(pos_elements);
1234 end
1235
1236 %elementstype
1237 if ~isnan(md.flowequation.element_equation)
1238 oldelements_type=md.flowequation.element_equation;
1239 md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1240 end
1241
1242 %connectivity
1243 md.mesh.elementconnectivity=NaN;
1244
1245 %materials
1246 if ~isnan(md.materials.rheology_n),
1247 md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1248 end
1249
1250 %increase connectivity if less than 25:
1251 if md.mesh.average_vertex_connectivity<=25,
1252 md.mesh.average_vertex_connectivity=100;
1253 end
1254 end % }}}
1255 function disp(self) % {{{
1256 disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
1257 disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
1258 disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1259 disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
1260 disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
1261 disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
1262 disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
1263 disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
1264 disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
1265 disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
1266 disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
1267 disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
1268 disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
1269 disp(sprintf('%19s: %-22s -- %s','slr' ,['[1x1 ' class(self.slr) ']'],'slr forcings'));
1270 disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
1271 disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
1272 disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
1273 disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
1274 disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
1275 disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
1276 disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
1277 disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
1278 disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
1279 disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
1280 disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
1281 disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
1282 disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
1283 disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
1284 disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
1285 disp(sprintf('%19s: %-22s -- %s','giaivins' ,['[1x1 ' class(self.giaivins) ']'],'parameters for giaivins solution'));
1286 disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
1287 disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
1288 disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
1289 disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
1290 disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
1291 disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
1292 disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
1293 disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
1294 end % }}}
1295 function memory(self) % {{{
1296
1297 disp(sprintf('\nMemory imprint:\n'));
1298
1299 fields=properties('model');
1300 mem=0;
1301
1302 for i=1:length(fields),
1303 field=self.(fields{i});
1304 s=whos('field');
1305 mem=mem+s.bytes/1e6;
1306 disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1307 end
1308 disp(sprintf('%19s--%10s','--------------','--------------'));
1309 disp(sprintf('%19s: %g Mb','Total',mem));
1310 end % }}}
1311 function netcdf(self,filename) % {{{
1312 %NETCDF - save model as netcdf
1313 %
1314 % Usage:
1315 % netcdf(md,filename)
1316 %
1317 % Example:
1318 % netcdf(md,'model.nc');
1319
1320 disp('Saving model as NetCDF');
1321 %1. Create NetCDF file
1322 ncid=netcdf.create(filename,'CLOBBER');
1323 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1324 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
1325 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1326 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1327
1328 %Preallocate variable id, needed to write variables in netcdf file
1329 var_id=zeros(1000,1);%preallocate
1330
1331 for step=1:2,
1332 counter=0;
1333 [var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
1334 if step==1, netcdf.endDef(ncid); end
1335 end
1336
1337 if counter>1000,
1338 warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1339 end
1340
1341 netcdf.close(ncid)
1342 end % }}}
1343 function xylim(self) % {{{
1344
1345 xlim([min(self.mesh.x) max(self.mesh.x)]);
1346 ylim([min(self.mesh.y) max(self.mesh.y)])
1347 end % }}}
1348 function md=upload(md) % {{{
1349 %the goal of this routine is to upload the model onto a server, and to empty it.
1350 %So first, save the model with a unique name and upload the file to the server:
1351 random_part=fix(rand(1)*10000);
1352 id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1353 eval(['save ' id ' md']);
1354
1355 %Now, upload the file:
1356 issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1357
1358 %Now, empty this model of everything except settings, and record name of file we just uploaded!
1359 settings_back=md.settings;
1360 md=model();
1361 md.settings=settings_back;
1362 md.settings.upload_filename=id;
1363
1364 %get locally rid of file that was uploaded
1365 eval(['delete ' id]);
1366
1367 end % }}}
1368 function md=download(md) % {{{
1369
1370 %the goal of this routine is to download the internals of the current model from a server, because
1371 %this model is empty, except for the settings which tell us where to go and find this model!
1372
1373 %Download the file:
1374 issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1375
1376 name=md.settings.upload_filename;
1377
1378 %Now, load this model:
1379 md=loadmodel(md.settings.upload_filename);
1380
1381 %get locally rid of file that was downloaded
1382 eval(['delete ' name]);
1383
1384 end % }}}
1385 function savemodeljs(md,modelname,websiteroot) % {{{
1386
1387 %the goal of this routine is to save the model as a javascript array that can be included in any html
1388 %file:
1389
1390 %disp:
1391 disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
1392
1393 %open file for writing and declare the model:
1394 fid=fopen([websiteroot '/js/' modelname '.js'],'w');
1395 fprintf(fid,'var %s=new model();\n',modelname);
1396
1397 %now go through all the classes and fwrite all the corresponding fields:
1398
1399 fields=properties('model');
1400 for i=1:length(fields),
1401 field=fields{i};
1402
1403 %Some properties do not need to be saved
1404 if ismember(field,{'results','cluster' }),
1405 continue;
1406 end
1407
1408 %Check that current field is an object
1409 if ~isobject(md.(field))
1410 error(['field ''' char(field) ''' is not an object']);
1411 end
1412
1413 %savemodeljs for current object
1414 %disp(['javascript saving ' field '...']);
1415 savemodeljs(md.(field),fid,modelname);
1416 end
1417
1418 %done, close file:
1419 fclose(fid);
1420 end
1421 end
1422 end
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