source: issm/trunk-jpl/src/m/classes/model.m@ 17754

Last change on this file since 17754 was 17754, checked in by Mathieu Morlighem, 11 years ago

NEW: better split in tetras
File size: 65.7 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 surfaceforcings = 0;
16 basalforcings = 0;
17 materials = 0;
18 damage = 0;
19 friction = 0;
20 flowequation = 0;
21 timestepping = 0;
22 initialization = 0;
23 rifts = 0;
24
25 debug = 0;
26 verbose = 0;
27 settings = 0;
28 toolkits = 0;
29 cluster = 0;
30
31 balancethickness = 0;
32 stressbalance = 0;
33 groundingline = 0;
34 hydrology = 0;
35 masstransport = 0;
36 thermal = 0;
37 steadystate = 0;
38 transient = 0;
39 gia = 0;
40
41 autodiff = 0;
42 flaim = 0;
43 inversion = 0;
44 qmu = 0;
45
46 results = 0;
47 outputdefinition = 0;
48 radaroverlay = 0;
49 miscellaneous = 0;
50 private = 0;
51
52 %}}}
53 end
54 methods (Static)
55 function md = loadobj(md) % {{{
56 % This function is directly called by matlab when a model object is
57 % loaded. If the input is a struct it is an old version of model and
58 % old fields must be recovered (make sure they are in the deprecated
59 % model properties)
60
61 if verLessThan('matlab','7.9'),
62 disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
63 disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
64
65 % This is a Matlab bug: all the fields of md have their default value
66 % Example of error message:
67 % Warning: Error loading an object of class 'model':
68 % Undefined function or method 'exist' for input arguments of type 'cell'
69 %
70 % This has been fixed in MATLAB 7.9 (R2009b) and later versions
71 end
72
73 if isstruct(md)
74 disp('Recovering model object from a previous version');
75 md = structtomodel(model,md);
76 end
77
78 %2012 August 4th
79 if isa(md.materials,'materials'),
80 disp('Recovering old materials');
81 if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
82 md.materials=matice(md.materials);
83 else
84 md.materials=matdamageice(md.materials);
85 end
86 end
87 %2013 April 12
88 if numel(md.stressbalance.loadingforce==1)
89 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
90 end
91 %2013 April 17
92 if isa(md.hydrology,'hydrology'),
93 disp('Recovering old hydrology class');
94 md.hydrology=hydrologyshreve(md.materials);
95 end
96 %2013 October 9
97 if ~isa(md.damage,'damage'),
98 md.damage=damage();
99 md.damage.D=zeros(md.mesh.numberofvertices,1);
100 md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
101 end
102 %2013 November 18
103 if ~isa(md.outputdefinition,'outputdefinition'),
104 md.outputdefinition=outputdefinition();
105 end
106 %2014 January 9th
107 if isa(md.surfaceforcings,'surfaceforcings'),
108 disp('Recovering old surfaceforcings class');
109 mass_balance=md.surfaceforcings.mass_balance;
110 md.surfaceforcings=SMB();
111 md.surfaceforcings.mass_balance=mass_balance;
112 end
113 %2014 March 26th
114 if isa(md.mesh,'mesh'),
115 disp('Recovering old mesh class');
116 if isprop(md.mesh,'dimension'),
117 if md.mesh.dimension==2,
118 md.mesh=mesh2d(md.mesh);
119 else
120 md.mesh=mesh3dprisms(md.mesh);
121 end
122 else
123 md.mesh=mesh2dvertical(md.mesh);
124 end
125 end
126 end% }}}
127 end
128 methods
129 function md = model(varargin) % {{{
130
131 switch nargin
132 case 0
133 md=setdefaultparameters(md);
134 otherwise
135 error('model constructor error message: 0 of 1 argument only in input.');
136 end
137 end
138 %}}}
139 function md = checkmessage(md,string) % {{{
140 if(nargout~=1) error('wrong usage, model must be an output'); end
141 disp(['model not consistent: ' string]);
142 md.private.isconsistent=false;
143 end
144 %}}}
145 function md = collapse(md)% {{{
146 %COLLAPSE - collapses a 3d mesh into a 2d mesh
147 %
148 % This routine collapses a 3d model into a 2d model
149 % and collapses all the fileds of the 3d model by
150 % taking their depth-averaged values
151 %
152 % Usage:
153 % md=collapse(md)
154 %
155 % See also: EXTRUDE, MODELEXTRACT
156
157 %Check that the model is really a 3d model
158 if ~strcmp(md.mesh.elementtype(),'Penta'),
159 error('collapse error message: only 3d mesh can be collapsed')
160 end
161
162 %Start with changing all the fields from the 3d mesh
163
164 %drag is limited to nodes that are on the bedrock.
165 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
166
167 %p and q (same deal, except for element that are on the bedrock: )
168 md.friction.p=project2d(md,md.friction.p,1);
169 md.friction.q=project2d(md,md.friction.q,1);
170
171 %observations
172 if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
173 if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
174 if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
175 if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
176 if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
177 if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
178 if ~isnan(md.surfaceforcings.mass_balance),
179 md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers);
180 end;
181 if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
182
183 %results
184 if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
185 if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
186 if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
187 if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
188 if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
189
190 %gia
191 if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
192 if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
193
194 %elementstype
195 if ~isnan(md.flowequation.element_equation)
196 md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
197 md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
198 md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
199 md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
200 md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
201 end
202
203 %boundary conditions
204 md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
205 md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
206 md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
207 md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
208 md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
209 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
210 md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers)
211 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
212
213 %materials
214 md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
215 md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
216
217 %damage:
218 md.damage.D=DepthAverage(md,md.damage.D);
219
220 %special for thermal modeling:
221 md.basalforcings.melting_rate=project2d(md,md.basalforcings.melting_rate,1);
222 md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
223
224 %update of connectivity matrix
225 md.mesh.average_vertex_connectivity=25;
226
227 %Collapse the mesh
228 nodes2d=md.mesh.numberofvertices2d;
229 elements2d=md.mesh.numberofelements2d;
230
231 %parameters
232 md.geometry.surface=project2d(md,md.geometry.surface,1);
233 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
234 md.geometry.base=project2d(md,md.geometry.base,1);
235 md.geometry.bed=project2d(md,md.geometry.bed,1);
236 md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
237 md.mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
238 md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
239 md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
240
241 %lat long
242 if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
243 if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
244
245 %Initialize with the 2d mesh
246 mesh=mesh2d();
247 mesh.x=md.mesh.x2d;
248 mesh.y=md.mesh.y2d;
249 mesh.z=zeros(size(md.mesh.x2d));
250 mesh.numberofvertices=md.mesh.numberofvertices2d;
251 mesh.numberofelements=md.mesh.numberofelements2d;
252 mesh.elements=md.mesh.elements2d;
253 md.mesh=mesh;
254
255 %Keep a trace of lower and upper nodes
256 md.mesh.lowervertex=NaN;
257 md.mesh.uppervertex=NaN;
258 md.mesh.lowerelements=NaN;
259 md.mesh.upperelements=NaN;
260
261 %Remove old mesh
262 md.mesh.x2d=NaN;
263 md.mesh.y2d=NaN;
264 md.mesh.elements2d=NaN;
265 md.mesh.numberofelements2d=md.mesh.numberofelements;
266 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
267 md.mesh.numberoflayers=0;
268
269 end % }}}
270 function md2 = extract(md,area) % {{{
271 %extract - extract a model according to an Argus contour or flag list
272 %
273 % This routine extracts a submodel from a bigger model with respect to a given contour
274 % md must be followed by the corresponding exp file or flags list
275 % It can either be a domain file (argus type, .exp extension), or an array of element flags.
276 % If user wants every element outside the domain to be
277 % extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
278 % an empty string '' will be considered as an empty domain
279 % a string 'all' will be considered as the entire domain
280 %
281 % Usage:
282 % md2=extract(md,area);
283 %
284 % Examples:
285 % md2=extract(md,'Domain.exp');
286 %
287 % See also: EXTRUDE, COLLAPSE
288
289 %copy model
290 md1=md;
291
292 %some checks
293 if ((nargin~=2) | (nargout~=1)),
294 help extract
295 error('extract error message: bad usage');
296 end
297
298 %get elements that are inside area
299 flag_elem=FlagElements(md1,area);
300 if ~any(flag_elem),
301 error('extracted model is empty');
302 end
303
304 %kick out all elements with 3 dirichlets
305 spc_elem=find(~flag_elem);
306 spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
307 flag=ones(md1.mesh.numberofvertices,1);
308 flag(spc_node)=0;
309 pos=find(sum(flag(md1.mesh.elements),2)==0);
310 flag_elem(pos)=0;
311
312 %extracted elements and nodes lists
313 pos_elem=find(flag_elem);
314 pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
315
316 %keep track of some fields
317 numberofvertices1=md1.mesh.numberofvertices;
318 numberofelements1=md1.mesh.numberofelements;
319 numberofvertices2=length(pos_node);
320 numberofelements2=length(pos_elem);
321 flag_node=zeros(numberofvertices1,1);
322 flag_node(pos_node)=1;
323
324 %Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
325 Pelem=zeros(numberofelements1,1);
326 Pelem(pos_elem)=[1:numberofelements2]';
327 Pnode=zeros(numberofvertices1,1);
328 Pnode(pos_node)=[1:numberofvertices2]';
329
330 %renumber the elements (some nodes won't exist anymore)
331 elements_1=md1.mesh.elements;
332 elements_2=elements_1(pos_elem,:);
333 elements_2(:,1)=Pnode(elements_2(:,1));
334 elements_2(:,2)=Pnode(elements_2(:,2));
335 elements_2(:,3)=Pnode(elements_2(:,3));
336 if isa(md1.mesh,'mesh3dprisms'),
337 elements_2(:,4)=Pnode(elements_2(:,4));
338 elements_2(:,5)=Pnode(elements_2(:,5));
339 elements_2(:,6)=Pnode(elements_2(:,6));
340 end
341
342 %OK, now create the new model!
343
344 %take every field from model
345 md2=md1;
346
347 %automatically modify fields
348
349 %loop over model fields
350 model_fields=fields(md1);
351 for i=1:length(model_fields),
352 %get field
353 field=md1.(model_fields{i});
354 fieldsize=size(field);
355 if isobject(field), %recursive call
356 object_fields=fields(md1.(model_fields{i}));
357 for j=1:length(object_fields),
358 %get field
359 field=md1.(model_fields{i}).(object_fields{j});
360 fieldsize=size(field);
361 %size = number of nodes * n
362 if fieldsize(1)==numberofvertices1
363 md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
364 elseif (fieldsize(1)==numberofvertices1+1)
365 md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
366 %size = number of elements * n
367 elseif fieldsize(1)==numberofelements1
368 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
369 end
370 end
371 else
372 %size = number of nodes * n
373 if fieldsize(1)==numberofvertices1
374 md2.(model_fields{i})=field(pos_node,:);
375 elseif (fieldsize(1)==numberofvertices1+1)
376 md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
377 %size = number of elements * n
378 elseif fieldsize(1)==numberofelements1
379 md2.(model_fields{i})=field(pos_elem,:);
380 end
381 end
382 end
383
384 %modify some specific fields
385
386 %Mesh
387 md2.mesh.numberofelements=numberofelements2;
388 md2.mesh.numberofvertices=numberofvertices2;
389 md2.mesh.elements=elements_2;
390
391 %mesh.uppervertex mesh.lowervertex
392 if isa(md1.mesh,'mesh3dprisms'),
393 md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
394 pos=find(~isnan(md2.mesh.uppervertex));
395 md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
396
397 md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
398 pos=find(~isnan(md2.mesh.lowervertex));
399 md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
400
401 md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
402 pos=find(~isnan(md2.mesh.upperelements));
403 md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
404
405 md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
406 pos=find(~isnan(md2.mesh.lowerelements));
407 md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
408 end
409
410 %Initial 2d mesh
411 if isa(md1.mesh,'mesh3dprisms'),
412 flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
413 pos_elem_2d=find(flag_elem_2d);
414 flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
415 pos_node_2d=find(flag_node_2d);
416
417 md2.mesh.numberofelements2d=length(pos_elem_2d);
418 md2.mesh.numberofvertices2d=length(pos_node_2d);
419 md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
420 md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
421 md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
422 md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
423
424 md2.mesh.x2d=md1.mesh.x(pos_node_2d);
425 md2.mesh.y2d=md1.mesh.y(pos_node_2d);
426 end
427
428 %Edges
429 if(dimension(md.mesh)==2),
430 if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
431 %renumber first two columns
432 pos=find(md2.mesh.edges(:,4)~=-1);
433 md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
434 md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
435 md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
436 md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
437 %remove edges when the 2 vertices are not in the domain.
438 md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
439 %Replace all zeros by -1 in the last two columns
440 pos=find(md2.mesh.edges(:,3)==0);
441 md2.mesh.edges(pos,3)=-1;
442 pos=find(md2.mesh.edges(:,4)==0);
443 md2.mesh.edges(pos,4)=-1;
444 %Invert -1 on the third column with last column (Also invert first two columns!!)
445 pos=find(md2.mesh.edges(:,3)==-1);
446 md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
447 md2.mesh.edges(pos,4)=-1;
448 values=md2.mesh.edges(pos,2);
449 md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
450 md2.mesh.edges(pos,1)=values;
451 %Finally remove edges that do not belong to any element
452 pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
453 md2.mesh.edges(pos,:)=[];
454 end
455 end
456
457 %Penalties
458 if ~isnan(md2.stressbalance.vertex_pairing),
459 for i=1:size(md1.stressbalance.vertex_pairing,1);
460 md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
461 end
462 md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
463 end
464 if ~isnan(md2.masstransport.vertex_pairing),
465 for i=1:size(md1.masstransport.vertex_pairing,1);
466 md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
467 end
468 md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
469 end
470
471 %recreate segments
472 if isa(md1.mesh,'mesh2d'),
473 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
474 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
475 md2.mesh.segments=contourenvelope(md2);
476 md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
477 else
478 %First do the connectivity for the contourenvelope in 2d
479 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
480 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
481 segments=contourenvelope(md2);
482 md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
483 md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
484 %Then do it for 3d as usual
485 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
486 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
487 end
488
489 %Boundary conditions: Dirichlets on new boundary
490 %Catch the elements that have not been extracted
491 orphans_elem=find(~flag_elem);
492 orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
493 %Figure out which node are on the boundary between md2 and md1
494 nodestoflag1=intersect(orphans_node,pos_node);
495 nodestoflag2=Pnode(nodestoflag1);
496 if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
497 if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
498 md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
499 md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
500 else
501 md2.stressbalance.spcvx(nodestoflag2)=NaN;
502 md2.stressbalance.spcvy(nodestoflag2)=NaN;
503 disp(' ')
504 disp('!! extract warning: spc values should be checked !!')
505 disp(' ')
506 end
507 %put 0 for vz
508 md2.stressbalance.spcvz(nodestoflag2)=0;
509 end
510 if ~isnan(md1.thermal.spctemperature),
511 md2.thermal.spctemperature(nodestoflag2,1)=1;
512 end
513
514 %Results fields
515 if isstruct(md1.results),
516 md2.results=struct();
517 solutionfields=fields(md1.results);
518 for i=1:length(solutionfields),
519 if isstruct(md1.results.(solutionfields{i}))
520 %get subfields
521 solutionsubfields=fields(md1.results.(solutionfields{i}));
522 for j=1:length(solutionsubfields),
523 field=md1.results.(solutionfields{i}).(solutionsubfields{j});
524 if length(field)==numberofvertices1,
525 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
526 elseif length(field)==numberofelements1,
527 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
528 else
529 md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
530 end
531 end
532 else
533 field=md1.results.(solutionfields{i});
534 if length(field)==numberofvertices1,
535 md2.results.(solutionfields{i})=field(pos_node);
536 elseif length(field)==numberofelements1,
537 md2.results.(solutionfields{i})=field(pos_elem);
538 else
539 md2.results.(solutionfields{i})=field;
540 end
541 end
542 end
543 end
544
545 %Keep track of pos_node and pos_elem
546 md2.mesh.extractedvertices=pos_node;
547 md2.mesh.extractedelements=pos_elem;
548 end % }}}
549 function md = extrude(md,varargin) % {{{
550 %EXTRUDE - vertically extrude a 2d mesh
551 %
552 % vertically extrude a 2d mesh and create corresponding 3d mesh.
553 % The vertical distribution can:
554 % - follow a polynomial law
555 % - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
556 % - be discribed by a list of coefficients (between 0 and 1)
557 %
558 %
559 % Usage:
560 % md=extrude(md,numlayers,extrusionexponent);
561 % md=extrude(md,numlayers,lowerexponent,upperexponent);
562 % md=extrude(md,listofcoefficients);
563 %
564 % Example:
565 % md=extrude(md,8,3);
566 % md=extrude(md,8,3,2);
567 % md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
568 %
569 % See also: MODELEXTRACT, COLLAPSE
570
571 %some checks on list of arguments
572 if ((nargin>4) | (nargin<2) | (nargout~=1)),
573 help extrude;
574 error('extrude error message');
575 end
576
577 %Extrude the mesh
578 if nargin==2, %list of coefficients
579 clist=varargin{1};
580 if any(clist<0) | any(clist>1),
581 error('extrusioncoefficients must be between 0 and 1');
582 end
583 extrusionlist=sort(unique([clist(:);0;1]));
584 numlayers=length(extrusionlist);
585 elseif nargin==3, %one polynomial law
586 if varargin{2}<=0,
587 help extrude;
588 error('extrusionexponent must be >=0');
589 end
590 numlayers=varargin{1};
591 extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
592 elseif nargin==4, %two polynomial laws
593 numlayers=varargin{1};
594 lowerexp=varargin{2};
595 upperexp=varargin{3};
596
597 if varargin{2}<=0 | varargin{3}<=0,
598 help extrude;
599 error('lower and upper extrusionexponents must be >=0');
600 end
601
602 lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
603 upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
604 extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
605
606 end
607
608 if numlayers<2,
609 error('number of layers should be at least 2');
610 end
611 if strcmp(md.mesh.domaintype(),'3D')
612 error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
613 end
614
615 %Initialize with the 2d mesh
616 mesh2d = md.mesh;
617 md.mesh=mesh3dprisms();
618 md.mesh.x = mesh2d.x;
619 md.mesh.y = mesh2d.y;
620 md.mesh.elements = mesh2d.elements;
621 md.mesh.numberofelements = mesh2d.numberofelements;
622 md.mesh.numberofvertices = mesh2d.numberofvertices;
623
624 md.mesh.lat = mesh2d.lat;
625 md.mesh.long = mesh2d.long;
626 md.mesh.hemisphere = mesh2d.hemisphere;
627
628 md.mesh.vertexonboundary = mesh2d.vertexonboundary;
629 md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
630 md.mesh.elementconnectivity = mesh2d.elementconnectivity;
631 md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
632
633 md.mesh.extractedvertices = mesh2d.extractedvertices;
634 md.mesh.extractedelements = mesh2d.extractedelements;
635
636 x3d=[];
637 y3d=[];
638 z3d=[]; %the lower node is on the bed
639 thickness3d=md.geometry.thickness; %thickness and bed for these nodes
640 bed3d=md.geometry.base;
641
642 %Create the new layers
643 for i=1:numlayers,
644 x3d=[x3d; md.mesh.x];
645 y3d=[y3d; md.mesh.y];
646 %nodes are distributed between bed and surface accordingly to the given exponent
647 z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
648 end
649 number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
650
651 %Extrude elements
652 elements3d=[];
653 for i=1:numlayers-1,
654 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
655 end
656 number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
657
658 %Keep a trace of lower and upper nodes
659 lowervertex=NaN*ones(number_nodes3d,1);
660 uppervertex=NaN*ones(number_nodes3d,1);
661 lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
662 uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
663 md.mesh.lowervertex=lowervertex;
664 md.mesh.uppervertex=uppervertex;
665
666 %same for lower and upper elements
667 lowerelements=NaN*ones(number_el3d,1);
668 upperelements=NaN*ones(number_el3d,1);
669 lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
670 upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
671 md.mesh.lowerelements=lowerelements;
672 md.mesh.upperelements=upperelements;
673
674 %Save old mesh
675 md.mesh.x2d=md.mesh.x;
676 md.mesh.y2d=md.mesh.y;
677 md.mesh.elements2d=md.mesh.elements;
678 md.mesh.numberofelements2d=md.mesh.numberofelements;
679 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
680
681 %Build global 3d mesh
682 md.mesh.elements=elements3d;
683 md.mesh.x=x3d;
684 md.mesh.y=y3d;
685 md.mesh.z=z3d;
686 md.mesh.numberofelements=number_el3d;
687 md.mesh.numberofvertices=number_nodes3d;
688 md.mesh.numberoflayers=numlayers;
689
690 %Ok, now deal with the other fields from the 2d mesh:
691
692 %lat long
693 md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
694 md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
695
696 %drag coefficient is limited to nodes that are on the bedrock.
697 md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1);
698
699 %p and q (same deal, except for element that are on the bedrock: )
700 md.friction.p=project3d(md,'vector',md.friction.p,'type','element');
701 md.friction.q=project3d(md,'vector',md.friction.q,'type','element');
702
703 %observations
704 md.inversion.vx_obs=project3d(md,'vector',md.inversion.vx_obs,'type','node');
705 md.inversion.vy_obs=project3d(md,'vector',md.inversion.vy_obs,'type','node');
706 md.inversion.vel_obs=project3d(md,'vector',md.inversion.vel_obs,'type','node');
707 md.inversion.thickness_obs=project3d(md,'vector',md.inversion.thickness_obs,'type','node');
708 md.surfaceforcings = extrude(md.surfaceforcings,md);
709 md.balancethickness.thickening_rate=project3d(md,'vector',md.balancethickness.thickening_rate,'type','node');
710
711 %results
712 if ~isnan(md.initialization.vx),md.initialization.vx=project3d(md,'vector',md.initialization.vx,'type','node');end;
713 if ~isnan(md.initialization.vy),md.initialization.vy=project3d(md,'vector',md.initialization.vy,'type','node');end;
714 if ~isnan(md.initialization.vz),md.initialization.vz=project3d(md,'vector',md.initialization.vz,'type','node');end;
715 if ~isnan(md.initialization.vel),md.initialization.vel=project3d(md,'vector',md.initialization.vel,'type','node');end;
716 if ~isnan(md.initialization.temperature),md.initialization.temperature=project3d(md,'vector',md.initialization.temperature,'type','node');end;
717 if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project3d(md,'vector',md.initialization.waterfraction,'type','node');end;
718 if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project3d(md,'vector',md.initialization.watercolumn,'type','node','layer',1);end;
719 if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project3d(md,'vector',md.initialization.sediment_head,'type','node','layer',1);end;
720 if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project3d(md,'vector',md.initialization.epl_head,'type','node','layer',1);end;
721 if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project3d(md,'vector',md.initialization.epl_thickness,'type','node','layer',1);end;
722
723 %bedinfo and surface info
724 md.mesh.elementonbase=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',1);
725 md.mesh.elementonsurface=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',md.mesh.numberoflayers-1);
726 md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
727 md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
728
729 %elementstype
730 if ~isnan(md.flowequation.element_equation)
731 oldelements_type=md.flowequation.element_equation;
732 md.flowequation.element_equation=zeros(number_el3d,1);
733 md.flowequation.element_equation=project3d(md,'vector',oldelements_type,'type','element');
734 end
735
736 %verticestype
737 if ~isnan(md.flowequation.vertex_equation)
738 oldvertices_type=md.flowequation.vertex_equation;
739 md.flowequation.vertex_equation=zeros(number_nodes3d,1);
740 md.flowequation.vertex_equation=project3d(md,'vector',oldvertices_type,'type','node');
741 end
742 md.flowequation.borderSSA=project3d(md,'vector',md.flowequation.borderSSA,'type','node');
743 md.flowequation.borderHO=project3d(md,'vector',md.flowequation.borderHO,'type','node');
744 md.flowequation.borderFS=project3d(md,'vector',md.flowequation.borderFS,'type','node');
745
746 %boundary conditions
747 md.stressbalance.spcvx=project3d(md,'vector',md.stressbalance.spcvx,'type','node');
748 md.stressbalance.spcvy=project3d(md,'vector',md.stressbalance.spcvy,'type','node');
749 md.stressbalance.spcvz=project3d(md,'vector',md.stressbalance.spcvz,'type','node');
750 md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',NaN);
751 if (length(md.initialization.temperature)==md.mesh.numberofvertices),
752 md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1);
753 if isprop(md.mesh,'vertexonsurface'),
754 pos=find(md.mesh.vertexonsurface);
755 md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface
756 end
757 end
758 md.masstransport.spcthickness=project3d(md,'vector',md.masstransport.spcthickness,'type','node');
759 md.masstransport.calvingrate=project3d(md,'vector',md.masstransport.calvingrate,'type','node');
760 md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
761 md.damage.spcdamage=project3d(md,'vector',md.damage.spcdamage,'type','node');
762 md.stressbalance.referential=project3d(md,'vector',md.stressbalance.referential,'type','node');
763 md.stressbalance.loadingforce=project3d(md,'vector',md.stressbalance.loadingforce,'type','node');
764
765 % Hydrologydc variables
766 if isa(md.hydrology,'hydrologydc');
767 md.hydrology.spcsediment_head=project3d(md,'vector',md.hydrology.spcsediment_head,'type','node','layer',1);
768 md.hydrology.spcepl_head=project3d(md,'vector',md.hydrology.spcepl_head,'type','node','layer',1);
769 md.hydrology.mask_eplactive_node=project3d(md,'vector',md.hydrology.mask_eplactive_node,'type','node','layer',1);
770 md.hydrology.sediment_transmitivity=project3d(md,'vector',md.hydrology.sediment_transmitivity,'type','node','layer',1);
771 md.hydrology.basal_moulin_input=project3d(md,'vector',md.hydrology.basal_moulin_input,'type','node','layer',1);
772 end
773
774 %connectivity
775 md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
776 md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
777 for i=2:numlayers-1,
778 md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
779 =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
780 end
781 md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
782
783 %materials
784 md.materials.rheology_B=project3d(md,'vector',md.materials.rheology_B,'type','node');
785 md.materials.rheology_n=project3d(md,'vector',md.materials.rheology_n,'type','element');
786
787 %damage
788 md.damage.D=project3d(md,'vector',md.damage.D,'type','node');
789
790 %parameters
791 md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
792 md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
793 md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node');
794 md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node');
795 md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
796 md.geometry.base=project3d(md,'vector',md.geometry.base,'type','node');
797 md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
798 md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
799 md.mask.groundedice_levelset=project3d(md,'vector',md.mask.groundedice_levelset,'type','node');
800 md.mask.ice_levelset=project3d(md,'vector',md.mask.ice_levelset,'type','node');
801 if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end;
802 if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end;
803 if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end;
804 if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end
805
806 %Put lithostatic pressure if there is an existing pressure
807 if ~isnan(md.initialization.pressure),
808 md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z);
809 end
810
811 %special for thermal modeling:
812 md.basalforcings.melting_rate=project3d(md,'vector',md.basalforcings.melting_rate,'type','node','layer',1);
813 if ~isnan(md.basalforcings.geothermalflux)
814 md.basalforcings.geothermalflux=project3d(md,'vector',md.basalforcings.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux
815 end
816
817 %increase connectivity if less than 25:
818 if md.mesh.average_vertex_connectivity<=25,
819 md.mesh.average_vertex_connectivity=100;
820 end
821 end % }}}
822 function md = structtomodel(md,structmd) % {{{
823
824 if ~isstruct(structmd) error('input model is not a structure'); end
825
826 %loaded model is a struct, initialize output and recover all fields
827 md = structtoobj(model,structmd);
828
829 %Old field now classes
830 if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
831 if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
832
833 %Field name change
834 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
835 if isfield(structmd,'p'), md.friction.p=structmd.p; end
836 if isfield(structmd,'q'), md.friction.q=structmd.p; end
837 if isfield(structmd,'melting'), md.basalforcings.melting_rate=structmd.melting; end
838 if isfield(structmd,'melting_rate'), md.basalforcings.melting_rate=structmd.melting_rate; end
839 if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
840 if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
841 if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
842 if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
843 if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
844 if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
845 if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
846 if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
847 if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
848 if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
849 if isfield(structmd,'g'), md.constants.g=structmd.g; end
850 if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
851 if isfield(structmd,'surface_mass_balance'), md.surfaceforcings.mass_balance=structmd.surface_mass_balance; end
852 if isfield(structmd,'basal_melting_rate'), md.basalforcings.melting_rate=structmd.basal_melting_rate; end
853 if isfield(structmd,'basal_melting_rate_correction'), md.basalforcings.melting_rate_correction=structmd.basal_melting_rate_correction; end
854 if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
855 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
856 if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
857 if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
858 if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
859 if isfield(structmd,'riftproperties'), %old implementation
860 md.rifts=rifts();
861 md.rifts.riftproperties=structmd.riftproperties;
862 md.rifts.riftstruct=structmd.rifts;
863 md.rifts.riftproperties=structmd.riftinfo;
864 end
865 if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
866 if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
867 if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
868 if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
869 if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
870 if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
871 if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
872 if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
873 if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
874 if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
875 if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
876 if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
877 if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
878 if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
879 if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
880 if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
881 if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
882 if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
883 if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
884 if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
885 if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
886 if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
887 if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
888 if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
889 if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
890 if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
891 if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
892 if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
893 if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
894 if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
895 if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
896 if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
897 if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
898 if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
899 if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
900 if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
901 if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
902 if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
903 if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
904 if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
905 if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
906 if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
907 if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
908 if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
909 if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
910 if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
911 if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
912 if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
913 if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
914 if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
915 if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
916 if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
917 if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
918 if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
919 if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
920 if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
921 if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
922 if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
923 if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
924 if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
925 if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
926 if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
927 if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
928 if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
929 if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
930 if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
931 if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
932 if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
933 if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
934 if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
935 if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
936 if isfield(structmd,'hemisphere'), md.mesh.hemisphere=structmd.hemisphere; end
937 if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
938 if isfield(structmd,'long'), md.mesh.long=structmd.long; end
939 if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
940 if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
941 if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
942 if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
943 if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
944 if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
945 if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
946 if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
947 if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
948 if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
949 if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
950 if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
951 if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
952 if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
953 if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
954 if isfield(structmd,'elementonbase'), md.mesh.elementonbase=structmd.elementonbase; end
955 if isfield(structmd,'elementonsurface'), md.mesh.elementonsurface=structmd.elementonsurface; end
956 if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
957 if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
958 if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
959 if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
960 if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
961 if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
962 if isfield(structmd,'edges'),
963 md.mesh.edges=structmd.edges;
964 md.mesh.edges(isnan(md.mesh.edges))=-1;
965 end
966 if isfield(structmd,'y'), md.mesh.y=structmd.y; end
967 if isfield(structmd,'x'), md.mesh.x=structmd.x; end
968 if isfield(structmd,'z'), md.mesh.z=structmd.z; end
969 if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
970 if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
971 if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
972 if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
973
974 if isnumeric(md.verbose),
975 md.verbose=verbose;
976 end
977
978 if isfield(structmd,'spcvelocity'),
979 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
980 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
981 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
982 pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
983 pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
984 pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
985 end
986 if isfield(structmd,'spcvx'),
987 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
988 pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
989 end
990 if isfield(structmd,'spcvy'),
991 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
992 pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
993 end
994 if isfield(structmd,'spcvz'),
995 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
996 pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
997 end
998 if isfield(structmd,'pressureload'),
999 if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
1000 pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
1001 pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
1002 pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
1003 end
1004 end
1005 if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
1006 pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
1007 pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
1008 pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
1009 pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
1010 pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
1011 pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
1012 pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
1013 pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
1014 end
1015 if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
1016 pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
1017 pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
1018 pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
1019 pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
1020 pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
1021 pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
1022 pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
1023 pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
1024 end
1025 if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
1026 if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
1027 if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1028 if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1029 end
1030 if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1031 if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1032 if (structmd.groundingline_migration==273), md.groundingline.migration='AgressiveMigration'; end
1033 if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1034 end
1035 if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1036 if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1037 if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1038 if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1039 end
1040 if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1041 pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1042 pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1043 pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1044 pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1045 pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1046 pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1047 pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1048 pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1049 pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1050 end
1051
1052 if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1053 md.thermal.stabilization=2;
1054 md.masstransport.stabilization=1;
1055 md.balancethickness.stabilization=1;
1056 end
1057 if isnumeric(md.masstransport.hydrostatic_adjustment)
1058 if md.masstransport.hydrostatic_adjustment==269,
1059 md.masstransport.hydrostatic_adjustment='Incremental';
1060 else
1061 md.masstransport.hydrostatic_adjustment='Absolute';
1062 end
1063 end
1064
1065 %New fields
1066 if ~isfield(structmd,'upperelements');
1067 md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1068 md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1069 end
1070 if ~isfield(structmd,'lowerelements');
1071 md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1072 md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1073 end
1074 if ~isfield(structmd,'diagnostic_ref');
1075 md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
1076 end
1077 if ~isfield(structmd,'loadingforce');
1078 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
1079 end
1080
1081 %2013 August 9
1082 if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1083 disp('Recovering old prognostic class');
1084 md.masstransport=masstransport(structmd.prognostic);
1085 end
1086 %2013 August 9
1087 if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') || isa(structmd.diagnostic,'stressbalance')),
1088 disp('Recovering old diagnostic class');
1089 md.stressbalance=stressbalance(structmd.diagnostic);
1090 end
1091 end% }}}
1092 function md = setdefaultparameters(md) % {{{
1093
1094 %initialize subclasses
1095 md.mesh = mesh2d();
1096 md.mask = mask();
1097 md.constants = constants();
1098 md.geometry = geometry();
1099 md.initialization = initialization();
1100 md.surfaceforcings = SMB();
1101 md.basalforcings = basalforcings();
1102 md.friction = friction();
1103 md.rifts = rifts();
1104 md.timestepping = timestepping();
1105 md.groundingline = groundingline();
1106 md.materials = matice();
1107 md.damage = damage();
1108 md.flowequation = flowequation();
1109 md.debug = debug();
1110 md.verbose = verbose();
1111 md.settings = settings();
1112 md.toolkits = toolkits();
1113 md.cluster = generic();
1114 md.balancethickness = balancethickness();
1115 md.stressbalance = stressbalance();
1116 md.hydrology = hydrologyshreve();
1117 md.masstransport = masstransport();
1118 md.thermal = thermal();
1119 md.steadystate = steadystate();
1120 md.transient = transient();
1121 md.gia = gia();
1122 md.autodiff = autodiff();
1123 md.flaim = flaim();
1124 md.inversion = inversion();
1125 md.qmu = qmu();
1126 md.radaroverlay = radaroverlay();
1127 md.results = struct();
1128 md.outputdefinition = outputdefinition();
1129 md.miscellaneous = miscellaneous();
1130 md.private = private();
1131 end
1132 %}}}
1133 function md = tetras(md,varargin) % {{{
1134 %TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1135 %
1136 % Usage:
1137 % md=tetra(md)
1138
1139 if ~isa(md.mesh,'mesh3dprisms')
1140 error('mesh is not a 3d prismatic mesh');
1141 end
1142
1143 %Initialize tetra mesh
1144 md.mesh=mesh3dtetras(md.mesh);
1145
1146 %Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
1147 steiner = 0;
1148 nbv = md.mesh.numberofvertices;
1149 nbt = 3*md.mesh.numberofelements;
1150 elements = zeros(nbt,4);
1151 for i=1:md.mesh.numberofelements
1152 v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
1153 v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
1154 if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1155 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1156 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1157 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1158 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1159 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1160 elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
1161 elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
1162 elements(end+1,:) = [v2 v3 v5 v7];
1163 elements(end+1,:) = [v3 v5 v6 v7];
1164 elements(end+1,:) = [v1 v3 v6 v7];
1165 elements(end+1,:) = [v1 v4 v6 v7];
1166 elements(end+1,:) = [v4 v5 v6 v7];
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 v4 v6];
1169 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1170 elements(3*(i-1)+3,:) = [v1 v2 v3 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 v2 v3 v4];
1173 elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
1174 elements(3*(i-1)+3,:) = [v3 v4 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 v2 v3 v4];
1177 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1178 elements(3*(i-1)+3,:) = [v2 v3 v4 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 v4 v5 v6];
1181 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1182 elements(3*(i-1)+3,:) = [v1 v3 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 v4 v5 v6];
1185 elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
1186 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1187 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1188 elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
1189 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1190 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1191 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1192 %NEW
1193 elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
1194 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1195 elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
1196 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1197 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1198 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1199 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1200 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1201 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1202 elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
1203 elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
1204 elements(end+1,:) = [v2 v5 v6 v7];
1205 elements(end+1,:) = [v2 v3 v6 v7];
1206 elements(end+1,:) = [v3 v4 v6 v7];
1207 elements(end+1,:) = [v1 v3 v4 v7];
1208 elements(end+1,:) = [v4 v5 v6 v7];
1209 else
1210 error('Case not supported'); %not supposed to happen!
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 disp([num2str(steiner) ' Steiner points had to be included'])
1219
1220 pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1221
1222 md.mesh.elements=elements;
1223 md.mesh.numberofelements=size(elements,1);
1224
1225 %p and q (same deal, except for element that are on the bedrock: )
1226 md.friction.p=md.friction.p(pos_elements);
1227 md.friction.q=md.friction.q(pos_elements);
1228
1229 %elementstype
1230 if ~isnan(md.flowequation.element_equation)
1231 oldelements_type=md.flowequation.element_equation;
1232 md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1233 end
1234
1235 %connectivity
1236 md.mesh.elementconnectivity=NaN;
1237
1238 %materials
1239 md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1240
1241 %increase connectivity if less than 25:
1242 if md.mesh.average_vertex_connectivity<=25,
1243 md.mesh.average_vertex_connectivity=100;
1244 end
1245 end % }}}
1246 function disp(obj) % {{{
1247 disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(obj.mesh) ']'],'mesh properties'));
1248 disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(obj.mask) ']'],'defines grounded and floating elements'));
1249 disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(obj.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1250 disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(obj.constants) ']'],'physical constants'));
1251 disp(sprintf('%19s: %-22s -- %s','surfaceforcings' ,['[1x1 ' class(obj.surfaceforcings) ']'],'surface forcings'));
1252 disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(obj.basalforcings) ']'],'bed forcings'));
1253 disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(obj.materials) ']'],'material properties'));
1254 disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(obj.damage) ']'],'parameters for damage evolution solution'));
1255 disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(obj.friction) ']'],'basal friction/drag properties'));
1256 disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(obj.flowequation) ']'],'flow equations'));
1257 disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(obj.timestepping) ']'],'time stepping for transient models'));
1258 disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(obj.initialization) ']'],'initial guess/state'));
1259 disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(obj.rifts) ']'],'rifts properties'));
1260 disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(obj.debug) ']'],'debugging tools (valgrind, gprof)'));
1261 disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
1262 disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
1263 disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(obj.toolkits) ']'],'PETSc options for each solution'));
1264 disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
1265 disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
1266 disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(obj.stressbalance) ']'],'parameters for stressbalance solution'));
1267 disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(obj.groundingline) ']'],'parameters for groundingline solution'));
1268 disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(obj.hydrology) ']'],'parameters for hydrology solution'));
1269 disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(obj.masstransport) ']'],'parameters for masstransport solution'));
1270 disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(obj.thermal) ']'],'parameters for thermal solution'));
1271 disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
1272 disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
1273 disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(obj.gia) ']'],'parameters for gia solution'));
1274 disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
1275 disp(sprintf('%19s: %-22s -- %s','flaim' ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
1276 disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(obj.inversion) ']'],'parameters for inverse methods'));
1277 disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(obj.qmu) ']'],'dakota properties'));
1278 disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(obj.outputdefinition) ']'],'output definition'));
1279 disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(obj.results) ']'],'model results'));
1280 disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(obj.radaroverlay) ']'],'radar image for plot overlay'));
1281 disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields'));
1282 end % }}}
1283 function memory(obj) % {{{
1284
1285 disp(sprintf('\nMemory imprint:\n'));
1286
1287 fields=properties('model');
1288 mem=0;
1289
1290 for i=1:length(fields),
1291 field=obj.(fields{i});
1292 s=whos('field');
1293 mem=mem+s.bytes/1e6;
1294 disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
1295 end
1296 disp(sprintf('%19s--%10s','--------------','--------------'));
1297 disp(sprintf('%19s: %g Mb','Total',mem));
1298 end % }}}
1299 function netcdf(obj,filename) % {{{
1300 %NETCDF - save model as netcdf
1301 %
1302 % Usage:
1303 % netcdf(md,filename)
1304 %
1305 % Example:
1306 % netcdf(md,'model.nc');
1307
1308 disp('Saving model as NetCDF');
1309 %1. Create NetCDF file
1310 ncid=netcdf.create(filename,'CLOBBER');
1311 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
1312 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' obj.miscellaneous.name ')']);
1313 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1314 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1315
1316 %Preallocate variable id, needed to write variables in netcdf file
1317 var_id=zeros(1000,1);%preallocate
1318
1319 for step=1:2,
1320 counter=0;
1321 [var_id,counter]=structtonc(ncid,'md',obj,0,var_id,counter,step);
1322 if step==1, netcdf.endDef(ncid); end
1323 end
1324
1325 if counter>1000,
1326 warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
1327 end
1328
1329 netcdf.close(ncid)
1330 end % }}}
1331 function xylim(obj) % {{{
1332
1333 xlim([min(obj.mesh.x) max(obj.mesh.x)]);
1334 ylim([min(obj.mesh.y) max(obj.mesh.y)])
1335 end % }}}
1336 function md=upload(md) % {{{
1337 %the goal of this routine is to upload the model onto a server, and to empty it.
1338 %So first, save the model with a unique name and upload the file to the server:
1339 random_part=fix(rand(1)*10000);
1340 id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1341 eval(['save ' id ' md']);
1342
1343 %Now, upload the file:
1344 issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1345
1346 %Now, empty this model of everything except settings, and record name of file we just uploaded!
1347 settings_back=md.settings;
1348 md=model();
1349 md.settings=settings_back;
1350 md.settings.upload_filename=id;
1351
1352 %get locally rid of file that was uploaded
1353 eval(['delete ' id]);
1354
1355 end % }}}
1356 function md=download(md) % {{{
1357
1358 %the goal of this routine is to download the internals of the current model from a server, because
1359 %this model is empty, except for the settings which tell us where to go and find this model!
1360
1361 %Download the file:
1362 issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1363
1364 name=md.settings.upload_filename;
1365
1366 %Now, load this model:
1367 md=loadmodel(md.settings.upload_filename);
1368
1369 %get locally rid of file that was downloaded
1370 eval(['delete ' name]);
1371
1372 end % }}}
1373 end
1374 end
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