source: issm/trunk-jpl/src/m/classes/model.m@ 21674

Last change on this file since 21674 was 21674, checked in by tsantos, 8 years ago

CHG: changes to add AMR capability; new class (amr.m) and new results (mesh). AMR capability in test.
File size: 65.0 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 gia = 0;
43 esa = 0;
44
45 autodiff = 0;
46 inversion = 0;
47 qmu = 0;
48 amr = 0;
49
50 results = 0;
51 outputdefinition = 0;
52 radaroverlay = 0;
53 miscellaneous = 0;
54 private = 0;
55
56 %}}}
57 end
58 methods (Static)
59 function md = loadobj(md) % {{{
60 % This function is directly called by matlab when a model object is
61 % loaded. If the input is a struct it is an old version of model and
62 % old fields must be recovered (make sure they are in the deprecated
63 % model properties)
64
65 if verLessThan('matlab','7.9'),
66 disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
67 disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
68
69 % This is a Matlab bug: all the fields of md have their default value
70 % Example of error message:
71 % Warning: Error loading an object of class 'model':
72 % Undefined function or method 'exist' for input arguments of type 'cell'
73 %
74 % This has been fixed in MATLAB 7.9 (R2009b) and later versions
75 end
76
77 if isstruct(md)
78 disp('Recovering model object from a previous version');
79 md = structtomodel(model,md);
80 end
81
82 %2012 August 4th
83 if isa(md.materials,'materials'),
84 disp('Recovering old materials');
85 if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
86 md.materials=matice(md.materials);
87 else
88 md.materials=matdamageice(md.materials);
89 end
90 end
91 %2013 April 12
92 if numel(md.stressbalance.loadingforce==1)
93 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
94 end
95 %2013 April 17
96 if isa(md.hydrology,'hydrology'),
97 disp('Recovering old hydrology class');
98 md.hydrology=hydrologyshreve(md.materials);
99 end
100 %2013 October 9
101 if ~isa(md.damage,'damage'),
102 md.damage=damage();
103 md.damage.D=zeros(md.mesh.numberofvertices,1);
104 md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
105 end
106 %2013 November 18
107 if ~isa(md.outputdefinition,'outputdefinition'),
108 md.outputdefinition=outputdefinition();
109 end
110 %2014 March 26th
111 if isa(md.mesh,'mesh'),
112 disp('Recovering old mesh class');
113 if isprop(md.mesh,'dimension'),
114 if md.mesh.dimension==2,
115 md.mesh=mesh2d(md.mesh);
116 else
117 md.mesh=mesh3dprisms(md.mesh);
118 end
119 else
120 md.mesh=mesh2dvertical(md.mesh);
121 end
122 end
123 %2014 November 12
124 if isa(md.calving,'double');
125 md.calving=calving();
126 end
127 %2016 February 3
128 if isa(md.slr,'double');
129 md.slr=slr();
130 end
131 %2016 October 11
132 if isa(md.esa,'double');
133 md.esa=esa();
134 end
135 %2017 February 10th
136 if md.settings.solver_residue_threshold==0,
137 md.settings.solver_residue_threshold = 1e-6;
138 end
139 %2017 April 10th
140 if isa(md.gia,'gia');
141 md.gia=giaivins();
142 end
143
144 end% }}}
145 end
146 methods
147 function md = model(varargin) % {{{
148
149 switch nargin
150 case 0
151 md=setdefaultparameters(md);
152 case 1
153 error('model constructor not supported yet');
154
155 otherwise
156 error('model constructor error message: 0 of 1 argument only in input.');
157 end
158 end
159 %}}}
160 function md = checkmessage(md,string) % {{{
161 if(nargout~=1) error('wrong usage, model must be an output'); end
162 disp(['model not consistent: ' string]);
163 md.private.isconsistent=false;
164 end
165 %}}}
166 function md = collapse(md)% {{{
167 %COLLAPSE - collapses a 3d mesh into a 2d mesh
168 %
169 % This routine collapses a 3d model into a 2d model
170 % and collapses all the fileds of the 3d model by
171 % taking their depth-averaged values
172 %
173 % Usage:
174 % md=collapse(md)
175 %
176 % See also: EXTRUDE, MODELEXTRACT
177
178 %Check that the model is really a 3d model
179 if ~strcmp(md.mesh.elementtype(),'Penta'),
180 error('collapse error message: only 3d mesh can be collapsed')
181 end
182
183 %Start with changing all the fields from the 3d mesh
184
185 %dealing with the friciton law
186 %drag is limited to nodes that are on the bedrock.
187 if isa(md.friction,'friction'),
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 elseif isa(md.friction,'frictionhydro'),
192 md.friction.q=project2d(md,md.friction.q,1);
193 md.friction.C=project2d(md,md.friction.C,1);
194 md.friction.As=project2d(md,md.friction.As,1);
195 md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
196 elseif isa(md.friction,'frictionwaterlayer'),
197 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
198 md.friction.p=project2d(md,md.friction.p,1);
199 md.friction.q=project2d(md,md.friction.q,1);
200 md.friction.water_layer=project2d(md,md.friction.water_layer,1);
201 elseif isa(md.friction,'frictionweertman'),
202 md.friction.C=project2d(md,md.friction.C,1);
203 md.friction.m=project2d(md,md.friction.m,1);
204 elseif isa(md.friction,'frictionweertmantemp'),
205 md.friction.C=project2d(md,md.friction.C,1);
206 md.friction.m=project2d(md,md.friction.m,1);
207 else
208 disp('friction type not supported');
209 end
210
211 %observations
212 if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
213 if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
214 if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
215 if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
216 if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
217 if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
218 if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
219 md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
220 elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
221 md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
222 end;
223
224 %results
225 if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
226 if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
227 if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
228 if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
229 if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
230 if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
231 if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
232 if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
233 if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
234 if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
235 if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
236 %giaivins
237 if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
238 if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
239
240 %elementstype
241 if ~isnan(md.flowequation.element_equation)
242 md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
243 md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
244 md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
245 md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
246 md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
247 end
248
249 %boundary conditions
250 md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
251 md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
252 md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
253 md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
254 md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
255 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
256 if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
257 if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
258 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
259
260 % Hydrologydc variables
261 if isa(md.hydrology,'hydrologydc');
262 md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
263 md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
264 md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
265 md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
266 if(md.hydrology.isefficientlayer==1)
267 md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
268 end
269 end
270
271 %materials
272 md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
273 md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
274
275 %damage:
276 if md.damage.isdamage,
277 md.damage.D=DepthAverage(md,md.damage.D);
278 end
279
280 %special for thermal modeling:
281 if ~isnan(md.basalforcings.groundedice_melting_rate),
282 md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
283 end
284 if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
285 md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
286 end
287 md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
288
289 if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
290 md.calving.coeff=project2d(md,md.calving.coeff,1);
291 end
292 if isprop(md.calving,'meltingrate') & ~isnan(md.calving.meltingrate),
293 md.calving.meltingrate=project2d(md,md.calving.meltingrate,1);
294 end
295
296 %update of connectivity matrix
297 md.mesh.average_vertex_connectivity=25;
298
299 %Collapse the mesh
300 nodes2d=md.mesh.numberofvertices2d;
301 elements2d=md.mesh.numberofelements2d;
302
303 %parameters
304 md.geometry.surface=project2d(md,md.geometry.surface,1);
305 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
306 md.geometry.base=project2d(md,md.geometry.base,1);
307 if ~isnan(md.geometry.bed),
308 md.geometry.bed=project2d(md,md.geometry.bed,1);
309 end
310
311 if ~isnan(md.mask.groundedice_levelset),
312 md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
313 end
314 if ~isnan(md.mask.ice_levelset),
315 md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
316 end
317
318 %Initialize with the 2d mesh
319 mesh=mesh2d();
320 mesh.x=md.mesh.x2d;
321 mesh.y=md.mesh.y2d;
322 mesh.numberofvertices=md.mesh.numberofvertices2d;
323 mesh.numberofelements=md.mesh.numberofelements2d;
324 mesh.elements=md.mesh.elements2d;
325 if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end
326 if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end
327 mesh.epsg=md.mesh.epsg;
328 if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
329 if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
330 md.mesh=mesh;
331 md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
332 md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
333 md.mesh.segments=contourenvelope(md.mesh);
334
335 end % }}}
336 function md2 = extract(md,area) % {{{
337 %extract - extract a model according to an Argus contour or flag list
338 %
339 % This routine extracts a submodel from a bigger model with respect to a given contour
340 % md must be followed by the corresponding exp file or flags list
341 % It can either be a domain file (argus type, .exp extension), or an array of element flags.
342 % If user wants every element outside the domain to be
343 % extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
344 % an empty string '' will be considered as an empty domain
345 % a string 'all' will be considered as the entire domain
346 %
347 % Usage:
348 % md2=extract(md,area);
349 %
350 % Examples:
351 % md2=extract(md,'Domain.exp');
352 %
353 % See also: EXTRUDE, COLLAPSE
354
355 %copy model
356 md1=md;
357
358 %some checks
359 if ((nargin~=2) | (nargout~=1)),
360 help extract
361 error('extract error message: bad usage');
362 end
363
364 %get elements that are inside area
365 flag_elem=FlagElements(md1,area);
366 if ~any(flag_elem),
367 error('extracted model is empty');
368 end
369
370 %kick out all elements with 3 dirichlets
371 spc_elem=find(~flag_elem);
372 spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
373 flag=ones(md1.mesh.numberofvertices,1);
374 flag(spc_node)=0;
375 pos=find(sum(flag(md1.mesh.elements),2)==0);
376 flag_elem(pos)=0;
377
378 %extracted elements and nodes lists
379 pos_elem=find(flag_elem);
380 pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
381
382 %keep track of some fields
383 numberofvertices1=md1.mesh.numberofvertices;
384 numberofelements1=md1.mesh.numberofelements;
385 numberofvertices2=length(pos_node);
386 numberofelements2=length(pos_elem);
387 flag_node=zeros(numberofvertices1,1);
388 flag_node(pos_node)=1;
389
390 %Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
391 Pelem=zeros(numberofelements1,1);
392 Pelem(pos_elem)=[1:numberofelements2]';
393 Pnode=zeros(numberofvertices1,1);
394 Pnode(pos_node)=[1:numberofvertices2]';
395
396 %renumber the elements (some nodes won't exist anymore)
397 elements_1=md1.mesh.elements;
398 elements_2=elements_1(pos_elem,:);
399 elements_2(:,1)=Pnode(elements_2(:,1));
400 elements_2(:,2)=Pnode(elements_2(:,2));
401 elements_2(:,3)=Pnode(elements_2(:,3));
402 if isa(md1.mesh,'mesh3dprisms'),
403 elements_2(:,4)=Pnode(elements_2(:,4));
404 elements_2(:,5)=Pnode(elements_2(:,5));
405 elements_2(:,6)=Pnode(elements_2(:,6));
406 end
407
408 %OK, now create the new model!
409
410 %take every field from model
411 md2=md1;
412
413 %automatically modify fields
414
415 %loop over model fields
416 model_fields=fields(md1);
417 for i=1:length(model_fields),
418 %get field
419 field=md1.(model_fields{i});
420 fieldsize=size(field);
421 if isobject(field), %recursive call
422 object_fields=fields(md1.(model_fields{i}));
423 for j=1:length(object_fields),
424 %get field
425 field=md1.(model_fields{i}).(object_fields{j});
426 fieldsize=size(field);
427 %size = number of nodes * n
428 if fieldsize(1)==numberofvertices1
429 md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
430 elseif (fieldsize(1)==numberofvertices1+1)
431 md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
432 %size = number of elements * n
433 elseif fieldsize(1)==numberofelements1
434 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
435 elseif (fieldsize(1)==numberofelements1+1)
436 md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
437 end
438 end
439 else
440 %size = number of nodes * n
441 if fieldsize(1)==numberofvertices1
442 md2.(model_fields{i})=field(pos_node,:);
443 elseif (fieldsize(1)==numberofvertices1+1)
444 md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
445 %size = number of elements * n
446 elseif fieldsize(1)==numberofelements1
447 md2.(model_fields{i})=field(pos_elem,:);
448 elseif (fieldsize(1)==numberofelements1+1)
449 md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
450 end
451 end
452 end
453
454 %modify some specific fields
455
456 %Mesh
457 md2.mesh.numberofelements=numberofelements2;
458 md2.mesh.numberofvertices=numberofvertices2;
459 md2.mesh.elements=elements_2;
460
461 %mesh.uppervertex mesh.lowervertex
462 if isa(md1.mesh,'mesh3dprisms'),
463 md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
464 pos=find(~isnan(md2.mesh.uppervertex));
465 md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
466
467 md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
468 pos=find(~isnan(md2.mesh.lowervertex));
469 md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
470
471 md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
472 pos=find(~isnan(md2.mesh.upperelements));
473 md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
474
475 md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
476 pos=find(~isnan(md2.mesh.lowerelements));
477 md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
478 end
479
480 %Initial 2d mesh
481 if isa(md1.mesh,'mesh3dprisms'),
482 flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
483 pos_elem_2d=find(flag_elem_2d);
484 flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
485 pos_node_2d=find(flag_node_2d);
486
487 md2.mesh.numberofelements2d=length(pos_elem_2d);
488 md2.mesh.numberofvertices2d=length(pos_node_2d);
489 md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
490 md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
491 md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
492 md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
493
494 md2.mesh.x2d=md1.mesh.x(pos_node_2d);
495 md2.mesh.y2d=md1.mesh.y(pos_node_2d);
496 end
497
498 %Edges
499 if(dimension(md.mesh)==2),
500 if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
501 %renumber first two columns
502 pos=find(md2.mesh.edges(:,4)~=-1);
503 md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
504 md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
505 md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
506 md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
507 %remove edges when the 2 vertices are not in the domain.
508 md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
509 %Replace all zeros by -1 in the last two columns
510 pos=find(md2.mesh.edges(:,3)==0);
511 md2.mesh.edges(pos,3)=-1;
512 pos=find(md2.mesh.edges(:,4)==0);
513 md2.mesh.edges(pos,4)=-1;
514 %Invert -1 on the third column with last column (Also invert first two columns!!)
515 pos=find(md2.mesh.edges(:,3)==-1);
516 md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
517 md2.mesh.edges(pos,4)=-1;
518 values=md2.mesh.edges(pos,2);
519 md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
520 md2.mesh.edges(pos,1)=values;
521 %Finally remove edges that do not belong to any element
522 pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
523 md2.mesh.edges(pos,:)=[];
524 end
525 end
526
527 %Penalties
528 if ~isnan(md2.stressbalance.vertex_pairing),
529 for i=1:size(md1.stressbalance.vertex_pairing,1);
530 md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
531 end
532 md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
533 end
534 if ~isnan(md2.masstransport.vertex_pairing),
535 for i=1:size(md1.masstransport.vertex_pairing,1);
536 md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
537 end
538 md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
539 end
540
541 %recreate segments
542 if isa(md1.mesh,'mesh2d') | isa(md1.mesh','mesh3dsurface'),
543 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
544 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
545 md2.mesh.segments=contourenvelope(md2.mesh);
546 md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
547 else
548 %First do the connectivity for the contourenvelope in 2d
549 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
550 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
551 segments=contourenvelope(md2.mesh);
552 md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
553 md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
554 %Then do it for 3d as usual
555 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
556 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
557 end
558
559 %Boundary conditions: Dirichlets on new boundary
560 %Catch the elements that have not been extracted
561 orphans_elem=find(~flag_elem);
562 orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
563 %Figure out which node are on the boundary between md2 and md1
564 nodestoflag1=intersect(orphans_node,pos_node);
565 nodestoflag2=Pnode(nodestoflag1);
566 if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
567 if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
568 md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
569 md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
570 else
571 md2.stressbalance.spcvx(nodestoflag2)=NaN;
572 md2.stressbalance.spcvy(nodestoflag2)=NaN;
573 disp(' ')
574 disp('!! extract warning: spc values should be checked !!')
575 disp(' ')
576 end
577 %put 0 for vz
578 md2.stressbalance.spcvz(nodestoflag2)=0;
579 end
580 if ~isnan(md1.thermal.spctemperature),
581 md2.thermal.spctemperature(nodestoflag2,1)=1;
582 end
583
584 %Results fields
585 if isstruct(md1.results),
586 md2.results=struct();
587 solutionfields=fields(md1.results);
588 for i=1:length(solutionfields),
589 if isstruct(md1.results.(solutionfields{i}))
590 %get subfields
591 solutionsubfields=fields(md1.results.(solutionfields{i}));
592 for j=1:length(solutionsubfields),
593 field=md1.results.(solutionfields{i}).(solutionsubfields{j});
594 if length(field)==numberofvertices1,
595 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
596 elseif length(field)==numberofelements1,
597 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
598 else
599 md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
600 end
601 end
602 else
603 field=md1.results.(solutionfields{i});
604 if length(field)==numberofvertices1,
605 md2.results.(solutionfields{i})=field(pos_node);
606 elseif length(field)==numberofelements1,
607 md2.results.(solutionfields{i})=field(pos_elem);
608 else
609 md2.results.(solutionfields{i})=field;
610 end
611 end
612 end
613 end
614
615 %Keep track of pos_node and pos_elem
616 md2.mesh.extractedvertices=pos_node;
617 md2.mesh.extractedelements=pos_elem;
618 end % }}}
619 function md = extrude(md,varargin) % {{{
620 %EXTRUDE - vertically extrude a 2d mesh
621 %
622 % vertically extrude a 2d mesh and create corresponding 3d mesh.
623 % The vertical distribution can:
624 % - follow a polynomial law
625 % - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
626 % - be discribed by a list of coefficients (between 0 and 1)
627 %
628 %
629 % Usage:
630 % md=extrude(md,numlayers,extrusionexponent);
631 % md=extrude(md,numlayers,lowerexponent,upperexponent);
632 % md=extrude(md,listofcoefficients);
633 %
634 % Example:
635 % md=extrude(md,15,1.3);
636 % md=extrude(md,15,1.3,1.2);
637 % md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
638 %
639 % See also: MODELEXTRACT, COLLAPSE
640
641 %some checks on list of arguments
642 if ((nargin>4) | (nargin<2) | (nargout~=1)),
643 help extrude;
644 error('extrude error message');
645 end
646
647 %Extrude the mesh
648 if nargin==2, %list of coefficients
649 clist=varargin{1};
650 if any(clist<0) | any(clist>1),
651 error('extrusioncoefficients must be between 0 and 1');
652 end
653 extrusionlist=sort(unique([clist(:);0;1]));
654 numlayers=length(extrusionlist);
655 elseif nargin==3, %one polynomial law
656 if varargin{2}<=0,
657 help extrude;
658 error('extrusionexponent must be >=0');
659 end
660 numlayers=varargin{1};
661 extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
662 elseif nargin==4, %two polynomial laws
663 numlayers=varargin{1};
664 lowerexp=varargin{2};
665 upperexp=varargin{3};
666
667 if varargin{2}<=0 | varargin{3}<=0,
668 help extrude;
669 error('lower and upper extrusionexponents must be >=0');
670 end
671
672 lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
673 upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
674 extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
675
676 end
677
678 if numlayers<2,
679 error('number of layers should be at least 2');
680 end
681 if strcmp(md.mesh.domaintype(),'3D')
682 error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
683 end
684
685 %Initialize with the 2d mesh
686 mesh2d = md.mesh;
687 md.mesh=mesh3dprisms();
688 md.mesh.x = mesh2d.x;
689 md.mesh.y = mesh2d.y;
690 md.mesh.elements = mesh2d.elements;
691 md.mesh.numberofelements = mesh2d.numberofelements;
692 md.mesh.numberofvertices = mesh2d.numberofvertices;
693
694 md.mesh.lat = mesh2d.lat;
695 md.mesh.long = mesh2d.long;
696 md.mesh.epsg = mesh2d.epsg;
697
698 md.mesh.vertexonboundary = mesh2d.vertexonboundary;
699 md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
700 md.mesh.elementconnectivity = mesh2d.elementconnectivity;
701 md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
702
703 md.mesh.extractedvertices = mesh2d.extractedvertices;
704 md.mesh.extractedelements = mesh2d.extractedelements;
705
706 x3d=[];
707 y3d=[];
708 z3d=[]; %the lower node is on the bed
709 thickness3d=md.geometry.thickness; %thickness and bed for these nodes
710 bed3d=md.geometry.base;
711
712 %Create the new layers
713 for i=1:numlayers,
714 x3d=[x3d; md.mesh.x];
715 y3d=[y3d; md.mesh.y];
716 %nodes are distributed between bed and surface accordingly to the given exponent
717 z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
718 end
719 number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
720
721 %Extrude elements
722 elements3d=[];
723 for i=1:numlayers-1,
724 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
725 end
726 number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
727
728 %Keep a trace of lower and upper nodes
729 lowervertex=NaN*ones(number_nodes3d,1);
730 uppervertex=NaN*ones(number_nodes3d,1);
731 lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
732 uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
733 md.mesh.lowervertex=lowervertex;
734 md.mesh.uppervertex=uppervertex;
735
736 %same for lower and upper elements
737 lowerelements=NaN*ones(number_el3d,1);
738 upperelements=NaN*ones(number_el3d,1);
739 lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
740 upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
741 md.mesh.lowerelements=lowerelements;
742 md.mesh.upperelements=upperelements;
743
744 %Save old mesh
745 md.mesh.x2d=md.mesh.x;
746 md.mesh.y2d=md.mesh.y;
747 md.mesh.elements2d=md.mesh.elements;
748 md.mesh.numberofelements2d=md.mesh.numberofelements;
749 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
750
751 %Build global 3d mesh
752 md.mesh.elements=elements3d;
753 md.mesh.x=x3d;
754 md.mesh.y=y3d;
755 md.mesh.z=z3d;
756 md.mesh.numberofelements=number_el3d;
757 md.mesh.numberofvertices=number_nodes3d;
758 md.mesh.numberoflayers=numlayers;
759
760 %Ok, now deal with the other fields from the 2d mesh:
761
762 %bedinfo and surface info
763 md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
764 md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
765 md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
766
767 %lat long
768 md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
769 md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
770
771 md.geometry=extrude(md.geometry,md);
772 md.friction = extrude(md.friction,md);
773 md.inversion = extrude(md.inversion,md);
774 md.smb = extrude(md.smb,md);
775 md.initialization = extrude(md.initialization,md);
776
777 md.flowequation=md.flowequation.extrude(md);
778 md.stressbalance=extrude(md.stressbalance,md);
779 md.thermal=md.thermal.extrude(md);
780 md.masstransport=md.masstransport.extrude(md);
781 md.levelset=extrude(md.levelset,md);
782 md.calving=extrude(md.calving,md);
783 md.hydrology = extrude(md.hydrology,md);
784
785 %connectivity
786 if ~isnan(md.mesh.elementconnectivity)
787 md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
788 md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
789 for i=2:numlayers-1,
790 md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
791 =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
792 end
793 md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
794 end
795
796 md.materials=extrude(md.materials,md);
797 md.damage=extrude(md.damage,md);
798 md.mask=extrude(md.mask,md);
799 md.qmu=extrude(md.qmu,md);
800 md.basalforcings=extrude(md.basalforcings,md);
801
802 %increase connectivity if less than 25:
803 if md.mesh.average_vertex_connectivity<=25,
804 md.mesh.average_vertex_connectivity=100;
805 end
806 end % }}}
807 function md = structtomodel(md,structmd) % {{{
808
809 if ~isstruct(structmd) error('input model is not a structure'); end
810
811 %loaded model is a struct, initialize output and recover all fields
812 md = structtoobj(model,structmd);
813
814 %Old field now classes
815 if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
816 if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
817
818 %Field name change
819 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
820 if isfield(structmd,'p'), md.friction.p=structmd.p; end
821 if isfield(structmd,'q'), md.friction.q=structmd.p; end
822 if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
823 if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
824 if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
825 if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
826 if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
827 if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
828 if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
829 if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
830 if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
831 if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
832 if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
833 if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
834 if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
835 if isfield(structmd,'g'), md.constants.g=structmd.g; end
836 if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
837 if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
838 if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
839 if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
840 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
841 if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
842 if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
843 if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
844 if isfield(structmd,'riftproperties'), %old implementation
845 md.rifts=rifts();
846 md.rifts.riftproperties=structmd.riftproperties;
847 md.rifts.riftstruct=structmd.rifts;
848 md.rifts.riftproperties=structmd.riftinfo;
849 end
850 if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
851 if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
852 if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
853 if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
854 if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
855 if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
856 if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
857 if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
858 if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
859 if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
860 if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
861 if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
862 if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
863 if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
864 if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
865 if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
866 if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
867 if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
868 if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
869 if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
870 if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
871 if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
872 if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
873 if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
874 if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
875 if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
876 if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
877 if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
878 if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
879 if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
880 if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
881 if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
882 if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
883 if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
884 if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
885 if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
886 if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
887 if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
888 if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
889 if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
890 if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
891 if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
892 if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
893 if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
894 if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
895 if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
896 if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
897 if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
898 if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
899 if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
900 if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
901 if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
902 if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
903 if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
904 if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
905 if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
906 if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
907 if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
908 if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
909 if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
910 if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
911 if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
912 if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
913 if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
914 if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
915 if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
916 if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
917 if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
918 if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
919 if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
920 if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
921 if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
922 if isfield(structmd,'long'), md.mesh.long=structmd.long; end
923 if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
924 if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
925 if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
926 if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
927 if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
928 if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
929 if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
930 if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
931 if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
932 if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
933 if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
934 if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
935 if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
936 if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
937 if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
938 if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
939 if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
940 if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
941 if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
942 if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
943 if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
944 if isfield(structmd,'edges'),
945 md.mesh.edges=structmd.edges;
946 md.mesh.edges(isnan(md.mesh.edges))=-1;
947 end
948 if isfield(structmd,'y'), md.mesh.y=structmd.y; end
949 if isfield(structmd,'x'), md.mesh.x=structmd.x; end
950 if isfield(structmd,'z'), md.mesh.z=structmd.z; end
951 if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
952 if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
953 if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
954
955 if isnumeric(md.verbose),
956 md.verbose=verbose;
957 end
958
959 if isfield(structmd,'spcvelocity'),
960 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
961 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
962 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
963 pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
964 pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
965 pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
966 end
967 if isfield(structmd,'spcvx'),
968 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
969 pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
970 end
971 if isfield(structmd,'spcvy'),
972 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
973 pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
974 end
975 if isfield(structmd,'spcvz'),
976 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
977 pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
978 end
979 if isfield(structmd,'pressureload'),
980 if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
981 pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
982 pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
983 pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
984 end
985 end
986 if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
987 pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
988 pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
989 pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
990 pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
991 pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
992 pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
993 pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
994 pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
995 end
996 if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
997 pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
998 pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
999 pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
1000 pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
1001 pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
1002 pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
1003 pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
1004 pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
1005 end
1006 if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
1007 if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
1008 if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1009 if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1010 end
1011 if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1012 if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1013 if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
1014 if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1015 end
1016 if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1017 if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1018 if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1019 if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1020 end
1021 if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1022 pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1023 pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1024 pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1025 pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1026 pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1027 pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1028 pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1029 pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1030 pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1031 end
1032
1033 if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1034 md.thermal.stabilization=2;
1035 md.masstransport.stabilization=1;
1036 md.balancethickness.stabilization=1;
1037 end
1038 if isnumeric(md.masstransport.hydrostatic_adjustment)
1039 if md.masstransport.hydrostatic_adjustment==269,
1040 md.masstransport.hydrostatic_adjustment='Incremental';
1041 else
1042 md.masstransport.hydrostatic_adjustment='Absolute';
1043 end
1044 end
1045
1046 %New fields
1047 if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
1048 md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1049 md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1050 end
1051 if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
1052 md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1053 md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1054 end
1055 if ~isfield(structmd,'diagnostic_ref');
1056 md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1057 end
1058 if ~isfield(structmd,'loadingforce');
1059 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1060 end
1061
1062 %2013 August 9
1063 if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1064 disp('Recovering old prognostic class');
1065 md.masstransport=masstransport(structmd.prognostic);
1066 end
1067 %2013 August 9
1068 if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') || isa(structmd.diagnostic,'stressbalance')),
1069 disp('Recovering old diagnostic class');
1070 md.stressbalance=stressbalance(structmd.diagnostic);
1071 end
1072 %2014 January 9th
1073 if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
1074 disp('Recovering old surfaceforcings class');
1075 mass_balance=structmd.surfaceforcings.mass_balance;
1076 md.smb=SMB();
1077 md.smb.mass_balance=mass_balance;
1078 end
1079 %2015 September 10
1080 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
1081 disp('Recovering old SMB class');
1082 md.smb=SMBforcing(structmd.surfaceforcings);
1083 end
1084 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
1085 disp('Recovering old SMBhenning class');
1086 md.smb=SMBhenning(structmd.surfaceforcings);
1087 end
1088
1089 end% }}}
1090 function md = setdefaultparameters(md) % {{{
1091
1092 %initialize subclasses
1093 md.mesh = mesh2d();
1094 md.mask = mask();
1095 md.constants = constants();
1096 md.geometry = geometry();
1097 md.initialization = initialization();
1098 md.smb = SMBforcing();
1099 md.basalforcings = basalforcings();
1100 md.friction = friction();
1101 md.rifts = rifts();
1102 md.slr = slr();
1103 md.timestepping = timestepping();
1104 md.groundingline = groundingline();
1105 md.materials = matice();
1106 md.damage = damage();
1107 md.flowequation = flowequation();
1108 md.debug = debug();
1109 md.verbose = verbose();
1110 md.settings = settings();
1111 md.toolkits = toolkits();
1112 md.cluster = generic();
1113 md.balancethickness = balancethickness();
1114 md.stressbalance = stressbalance();
1115 md.hydrology = hydrologyshreve();
1116 md.masstransport = masstransport();
1117 md.thermal = thermal();
1118 md.steadystate = steadystate();
1119 md.transient = transient();
1120 md.levelset = levelset();
1121 md.calving = calving();
1122 md.gia = giaivins();
1123 md.esa = esa();
1124 md.autodiff = autodiff();
1125 md.inversion = inversion();
1126 md.qmu = qmu();
1127 md.amr = amr();
1128 md.radaroverlay = radaroverlay();
1129 md.results = struct();
1130 md.outputdefinition = outputdefinition();
1131 md.miscellaneous = miscellaneous();
1132 md.private = private();
1133 end
1134 %}}}
1135 function md = tetras(md,varargin) % {{{
1136 %TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1137 %
1138 % Usage:
1139 % md=tetra(md)
1140
1141 if ~isa(md.mesh,'mesh3dprisms')
1142 error('mesh is not a 3d prismatic mesh');
1143 end
1144
1145 %Initialize tetra mesh
1146 md.mesh=mesh3dtetras(md.mesh);
1147
1148 %Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
1149 steiner = 0;
1150 nbv = md.mesh.numberofvertices;
1151 nbt = 3*md.mesh.numberofelements;
1152 elements = zeros(nbt,4);
1153 for i=1:md.mesh.numberofelements
1154 v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
1155 v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
1156 if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1157 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1158 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1159 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1160 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1161 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1162 elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
1163 elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
1164 elements(end+1,:) = [v2 v3 v5 v7];
1165 elements(end+1,:) = [v3 v5 v6 v7];
1166 elements(end+1,:) = [v1 v3 v6 v7];
1167 elements(end+1,:) = [v1 v4 v6 v7];
1168 elements(end+1,:) = [v4 v5 v6 v7];
1169 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1170 elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
1171 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1172 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1173 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1174 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1175 elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
1176 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1177 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1178 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1179 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1180 elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
1181 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1182 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1183 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1184 elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
1185 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1186 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1187 elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
1188 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1189 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1190 elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
1191 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1192 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1193 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1194 elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
1195 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1196 elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
1197 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1198 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1199 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1200 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1201 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1202 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1203 elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
1204 elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
1205 elements(end+1,:) = [v2 v5 v6 v7];
1206 elements(end+1,:) = [v2 v3 v6 v7];
1207 elements(end+1,:) = [v3 v4 v6 v7];
1208 elements(end+1,:) = [v1 v3 v4 v7];
1209 elements(end+1,:) = [v4 v5 v6 v7];
1210 else
1211 error('Case not supported'); %not supposed to happen!
1212 end
1213 %Reorder elements to make sure they are direct
1214 for j=1:3
1215 element = elements(3*(i-1)+j,:);
1216 matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
1217 if det(matrix)>0,
1218 elements(3*(i-1)+j,1)=element(2);
1219 elements(3*(i-1)+j,2)=element(1);
1220 end
1221 end
1222 end
1223 %%Split in 3 tetras
1224 %subelement1 = [1 2 3 5];
1225 %subelement2 = [4 6 5 1];
1226 %subelement3 = [5 6 3 1];
1227 %elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
1228 if steiner==0,
1229 disp('No Steiner point required to split prismatic mesh into tets');
1230 else
1231 disp([num2str(steiner) ' Steiner points had to be included'])
1232 error('Steiner point not supported yet');
1233 end
1234
1235 pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1236
1237 md.mesh.elements=elements;
1238 md.mesh.numberofelements=size(elements,1);
1239
1240 %p and q (same deal, except for element that are on the bedrock: )
1241 if ~isnan(md.friction.p),
1242 md.friction.p=md.friction.p(pos_elements);
1243 md.friction.q=md.friction.q(pos_elements);
1244 end
1245
1246 %elementstype
1247 if ~isnan(md.flowequation.element_equation)
1248 oldelements_type=md.flowequation.element_equation;
1249 md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1250 end
1251
1252 %connectivity
1253 md.mesh.elementconnectivity=NaN;
1254
1255 %materials
1256 if ~isnan(md.materials.rheology_n),
1257 md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1258 end
1259
1260 %increase connectivity if less than 25:
1261 if md.mesh.average_vertex_connectivity<=25,
1262 md.mesh.average_vertex_connectivity=100;
1263 end
1264 end % }}}
1265 function disp(self) % {{{
1266 disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
1267 disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
1268 disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1269 disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
1270 disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
1271 disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
1272 disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
1273 disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
1274 disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
1275 disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
1276 disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
1277 disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
1278 disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
1279 disp(sprintf('%19s: %-22s -- %s','slr' ,['[1x1 ' class(self.slr) ']'],'slr forcings'));
1280 disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
1281 disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
1282 disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
1283 disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
1284 disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
1285 disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
1286 disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
1287 disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
1288 disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
1289 disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
1290 disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
1291 disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
1292 disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
1293 disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
1294 disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
1295 disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
1296 disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
1297 disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
1298 disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
1299 disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
1300 disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
1301 disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
1302 disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
1303 disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
1304 disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
1305 end % }}}
1306 function memory(self) % {{{
1307
1308 disp(sprintf('\nMemory imprint:\n'));
1309
1310 fields=properties('model');
1311 mem=0;
1312
1313 for i=1:length(fields),
1314 field=self.(fields{i});
1315 s=whos('field');
1316 mem=mem+s.bytes/1e6;
1317 disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1318 end
1319 disp(sprintf('%19s--%10s','--------------','--------------'));
1320 disp(sprintf('%19s: %g Mb','Total',mem));
1321 end % }}}
1322 function netcdf(self,filename) % {{{
1323 %NETCDF - save model as netcdf
1324 %
1325 % Usage:
1326 % netcdf(md,filename)
1327 %
1328 % Example:
1329 % netcdf(md,'model.nc');
1330
1331 disp('Saving model as NetCDF');
1332 %1. Create NetCDF file
1333 ncid=netcdf.create(filename,'CLOBBER');
1334 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1335 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
1336 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1337 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1338
1339 %Preallocate variable id, needed to write variables in netcdf file
1340 var_id=zeros(1000,1);%preallocate
1341
1342 for step=1:2,
1343 counter=0;
1344 [var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
1345 if step==1, netcdf.endDef(ncid); end
1346 end
1347
1348 if counter>1000,
1349 warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1350 end
1351
1352 netcdf.close(ncid)
1353 end % }}}
1354 function xylim(self) % {{{
1355
1356 xlim([min(self.mesh.x) max(self.mesh.x)]);
1357 ylim([min(self.mesh.y) max(self.mesh.y)])
1358 end % }}}
1359 function md=upload(md) % {{{
1360 %the goal of this routine is to upload the model onto a server, and to empty it.
1361 %So first, save the model with a unique name and upload the file to the server:
1362 random_part=fix(rand(1)*10000);
1363 id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1364 eval(['save ' id ' md']);
1365
1366 %Now, upload the file:
1367 issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1368
1369 %Now, empty this model of everything except settings, and record name of file we just uploaded!
1370 settings_back=md.settings;
1371 md=model();
1372 md.settings=settings_back;
1373 md.settings.upload_filename=id;
1374
1375 %get locally rid of file that was uploaded
1376 eval(['delete ' id]);
1377
1378 end % }}}
1379 function md=download(md) % {{{
1380
1381 %the goal of this routine is to download the internals of the current model from a server, because
1382 %this model is empty, except for the settings which tell us where to go and find this model!
1383
1384 %Download the file:
1385 issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1386
1387 name=md.settings.upload_filename;
1388
1389 %Now, load this model:
1390 md=loadmodel(md.settings.upload_filename);
1391
1392 %get locally rid of file that was downloaded
1393 eval(['delete ' name]);
1394
1395 end % }}}
1396 function savemodeljs(md,modelname,websiteroot) % {{{
1397
1398 %the goal of this routine is to save the model as a javascript array that can be included in any html
1399 %file:
1400
1401 %disp:
1402 disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
1403
1404 %open file for writing and declare the model:
1405 fid=fopen([websiteroot '/js/' modelname '.js'],'w');
1406 fprintf(fid,'var %s=new model();\n',modelname);
1407
1408 %now go through all the classes and fwrite all the corresponding fields:
1409
1410 fields=properties('model');
1411 for i=1:length(fields),
1412 field=fields{i};
1413
1414 %Some properties do not need to be saved
1415 if ismember(field,{'results','cluster' }),
1416 continue;
1417 end
1418
1419 %Check that current field is an object
1420 if ~isobject(md.(field))
1421 error(['field ''' char(field) ''' is not an object']);
1422 end
1423
1424 %savemodeljs for current object
1425 %disp(['javascript saving ' field '...']);
1426 savemodeljs(md.(field),fid,modelname);
1427 end
1428
1429 %done, close file:
1430 fclose(fid);
1431 end
1432 end
1433 end
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