source: issm/trunk-jpl/src/m/classes/model.m@ 17563

Last change on this file since 17563 was 17563, checked in by Mathieu Morlighem, 11 years ago

BUG: fixing some tests now that subclasses are used for md.mesh
File size: 62.3 KB
RevLine 
[8926]1%MODEL class definition
2%
3% Usage:
4% md = model(varargin)
5
6classdef model
[13692]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;
[9778]12
[13692]13 geometry = 0;
14 constants = 0;
15 surfaceforcings = 0;
16 basalforcings = 0;
17 materials = 0;
[16160]18 damage = 0;
[13692]19 friction = 0;
20 flowequation = 0;
21 timestepping = 0;
22 initialization = 0;
23 rifts = 0;
[9778]24
[13692]25 debug = 0;
26 verbose = 0;
27 settings = 0;
[14621]28 toolkits = 0;
[13692]29 cluster = 0;
[9778]30
[13692]31 balancethickness = 0;
[15771]32 stressbalance = 0;
[13692]33 groundingline = 0;
34 hydrology = 0;
[15767]35 masstransport = 0;
[13692]36 thermal = 0;
37 steadystate = 0;
38 transient = 0;
[14724]39 gia = 0;
[9778]40
[13692]41 autodiff = 0;
42 flaim = 0;
43 inversion = 0;
44 qmu = 0;
[8926]45
[13692]46 results = 0;
[16388]47 outputdefinition = 0;
[13692]48 radaroverlay = 0;
49 miscellaneous = 0;
50 private = 0;
[9778]51
[13692]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)
[8926]60
[13692]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');
[8952]64
[13692]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
[8952]72
[13692]73 if isstruct(md)
74 disp('Recovering model object from a previous version');
75 md = structtomodel(model,md);
76 end
[13239]77
[13692]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),
[13718]82 md.materials=matice(md.materials);
83 else
[13692]84 md.materials=matdamageice(md.materials);
85 end
86 end
[14559]87 %2013 April 12
[15771]88 if numel(md.stressbalance.loadingforce==1)
89 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14559]90 end
[14618]91 %2013 April 17
92 if isa(md.hydrology,'hydrology'),
93 disp('Recovering old hydrology class');
94 md.hydrology=hydrologyshreve(md.materials);
95 end
[16356]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
[16822]102 %2013 November 18
103 if ~isa(md.outputdefinition,'outputdefinition'),
104 md.outputdefinition=outputdefinition();
105 end
[17079]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
[17558]113 %2014 March 26th
114 if isa(md.mesh,'mesh'),
[17559]115 if(strcmp(meshtype(md.mesh),'2Dhorizontal')),
[17558]116 md.mesh=mesh2d(md.mesh);
117 else
118 md.mesh=mesh3dprisms(md.mesh);
119 end
120 end
[13692]121 end% }}}
122 end
123 methods
124 function md = model(varargin) % {{{
[8926]125
[13692]126 switch nargin
127 case 0
128 md=setdefaultparameters(md);
129 otherwise
130 error('model constructor error message: 0 of 1 argument only in input.');
131 end
132 end
133 %}}}
134 function md = checkmessage(md,string) % {{{
135 if(nargout~=1) error('wrong usage, model must be an output'); end
136 disp(['model not consistent: ' string]);
137 md.private.isconsistent=false;
138 end
139 %}}}
140 function md = collapse(md)% {{{
141 %COLLAPSE - collapses a 3d mesh into a 2d mesh
142 %
143 % This routine collapses a 3d model into a 2d model
144 % and collapses all the fileds of the 3d model by
145 % taking their depth-averaged values
146 %
147 % Usage:
148 % md=collapse(md)
149 %
150 % See also: EXTRUDE, MODELEXTRACT
[13005]151
[13692]152 %Check that the model is really a 3d model
[17558]153 if ~strcmp(md.mesh.meshtype(),'3D'),
[13692]154 error('collapse error message: only 3d mesh can be collapsed')
155 end
[13005]156
[13692]157 %Start with changing alle the fields from the 3d mesh
[13005]158
[13692]159 %drag is limited to nodes that are on the bedrock.
160 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
[13005]161
[13692]162 %p and q (same deal, except for element that are on the bedrock: )
163 md.friction.p=project2d(md,md.friction.p,1);
164 md.friction.q=project2d(md,md.friction.q,1);
[13005]165
[13692]166 %observations
167 if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
168 if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
169 if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
170 if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
171 if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
172 if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
173 if ~isnan(md.surfaceforcings.mass_balance),
174 md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers);
175 end;
176 if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
[13005]177
[13692]178 %results
179 if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
180 if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
181 if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
182 if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
183 if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[13005]184
[15021]185 %gia
186 if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
187 if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
188
[13692]189 %elementstype
190 if ~isnan(md.flowequation.element_equation)
191 md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
192 md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]193 md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
194 md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
195 md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]196 end
[13005]197
[13692]198 %boundary conditions
[15771]199 md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
200 md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
201 md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
202 md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
203 md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[15767]204 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
[16344]205 md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers)
[13692]206 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]207
[13692]208 %materials
209 md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
210 md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]211
212 %damage:
213 md.damage.D=DepthAverage(md,md.damage.D);
[13005]214
[13692]215 %special for thermal modeling:
216 md.basalforcings.melting_rate=project2d(md,md.basalforcings.melting_rate,1);
217 md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]218
[13692]219 %update of connectivity matrix
220 md.mesh.average_vertex_connectivity=25;
[13005]221
[13692]222 %Collapse the mesh
223 nodes2d=md.mesh.numberofvertices2d;
224 elements2d=md.mesh.numberofelements2d;
[13005]225
[13692]226 %parameters
227 md.geometry.surface=project2d(md,md.geometry.surface,1);
228 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
229 md.geometry.bed=project2d(md,md.geometry.bed,1);
230 md.geometry.bathymetry=project2d(md,md.geometry.bathymetry,1);
231 md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
232 md.mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
[15943]233 md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
234 md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
[13005]235
[13692]236 %lat long
237 if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
238 if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
[13005]239
[13692]240 %Initialize with the 2d mesh
[17558]241 md.mesh=mesh2d();
[13692]242 md.mesh.x=md.mesh.x2d;
243 md.mesh.y=md.mesh.y2d;
244 md.mesh.z=zeros(size(md.mesh.x2d));
245 md.mesh.numberofvertices=md.mesh.numberofvertices2d;
246 md.mesh.numberofelements=md.mesh.numberofelements2d;
247 md.mesh.elements=md.mesh.elements2d;
[13005]248
[13692]249 %Keep a trace of lower and upper nodes
250 md.mesh.lowervertex=NaN;
251 md.mesh.uppervertex=NaN;
252 md.mesh.lowerelements=NaN;
253 md.mesh.upperelements=NaN;
[13005]254
[13692]255 %Remove old mesh
256 md.mesh.x2d=NaN;
257 md.mesh.y2d=NaN;
258 md.mesh.elements2d=NaN;
259 md.mesh.numberofelements2d=md.mesh.numberofelements;
260 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
261 md.mesh.numberoflayers=0;
[13005]262
[13692]263 end % }}}
264 function md2 = extract(md,area) % {{{
265 %extract - extract a model according to an Argus contour or flag list
266 %
267 % This routine extracts a submodel from a bigger model with respect to a given contour
268 % md must be followed by the corresponding exp file or flags list
269 % It can either be a domain file (argus type, .exp extension), or an array of element flags.
270 % If user wants every element outside the domain to be
[15564]271 % extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]272 % an empty string '' will be considered as an empty domain
273 % a string 'all' will be considered as the entire domain
274 %
275 % Usage:
276 % md2=extract(md,area);
277 %
278 % Examples:
279 % md2=extract(md,'Domain.exp');
280 %
281 % See also: EXTRUDE, COLLAPSE
[13005]282
[13692]283 %copy model
284 md1=md;
[13005]285
[13692]286 %some checks
287 if ((nargin~=2) | (nargout~=1)),
288 help extract
289 error('extract error message: bad usage');
290 end
[13005]291
[13692]292 %get elements that are inside area
293 flag_elem=FlagElements(md1,area);
294 if ~any(flag_elem),
295 error('extracted model is empty');
296 end
[13005]297
[13692]298 %kick out all elements with 3 dirichlets
299 spc_elem=find(~flag_elem);
300 spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
301 flag=ones(md1.mesh.numberofvertices,1);
302 flag(spc_node)=0;
303 pos=find(sum(flag(md1.mesh.elements),2)==0);
304 flag_elem(pos)=0;
[13005]305
[13692]306 %extracted elements and nodes lists
307 pos_elem=find(flag_elem);
308 pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]309
[13692]310 %keep track of some fields
311 numberofvertices1=md1.mesh.numberofvertices;
312 numberofelements1=md1.mesh.numberofelements;
313 numberofvertices2=length(pos_node);
314 numberofelements2=length(pos_elem);
315 flag_node=zeros(numberofvertices1,1);
316 flag_node(pos_node)=1;
[13005]317
[13692]318 %Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
319 Pelem=zeros(numberofelements1,1);
320 Pelem(pos_elem)=[1:numberofelements2]';
321 Pnode=zeros(numberofvertices1,1);
322 Pnode(pos_node)=[1:numberofvertices2]';
[13005]323
[13857]324 %renumber the elements (some nodes won't exist anymore)
[13692]325 elements_1=md1.mesh.elements;
326 elements_2=elements_1(pos_elem,:);
327 elements_2(:,1)=Pnode(elements_2(:,1));
328 elements_2(:,2)=Pnode(elements_2(:,2));
329 elements_2(:,3)=Pnode(elements_2(:,3));
[17558]330 if isa(md1.mesh,'mesh3dprisms'),
[13692]331 elements_2(:,4)=Pnode(elements_2(:,4));
332 elements_2(:,5)=Pnode(elements_2(:,5));
333 elements_2(:,6)=Pnode(elements_2(:,6));
334 end
[13005]335
[13857]336 %OK, now create the new model!
[13005]337
[13857]338 %take every field from model
[13692]339 md2=md1;
[13005]340
[13692]341 %automatically modify fields
[13005]342
[13692]343 %loop over model fields
344 model_fields=fields(md1);
345 for i=1:length(model_fields),
346 %get field
347 field=md1.(model_fields{i});
348 fieldsize=size(field);
349 if isobject(field), %recursive call
350 object_fields=fields(md1.(model_fields{i}));
351 for j=1:length(object_fields),
352 %get field
353 field=md1.(model_fields{i}).(object_fields{j});
354 fieldsize=size(field);
355 %size = number of nodes * n
356 if fieldsize(1)==numberofvertices1
357 md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
358 elseif (fieldsize(1)==numberofvertices1+1)
359 md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]360 %size = number of elements * n
[13692]361 elseif fieldsize(1)==numberofelements1
362 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
363 end
364 end
365 else
366 %size = number of nodes * n
367 if fieldsize(1)==numberofvertices1
368 md2.(model_fields{i})=field(pos_node,:);
369 elseif (fieldsize(1)==numberofvertices1+1)
370 md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]371 %size = number of elements * n
[13692]372 elseif fieldsize(1)==numberofelements1
373 md2.(model_fields{i})=field(pos_elem,:);
374 end
375 end
376 end
[13005]377
[13692]378 %modify some specific fields
[13005]379
[13692]380 %Mesh
381 md2.mesh.numberofelements=numberofelements2;
382 md2.mesh.numberofvertices=numberofvertices2;
383 md2.mesh.elements=elements_2;
[13005]384
[13692]385 %mesh.uppervertex mesh.lowervertex
[17558]386 if isa(md1.mesh,'mesh3dprisms'),
[13692]387 md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
388 pos=find(~isnan(md2.mesh.uppervertex));
389 md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]390
[13692]391 md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
392 pos=find(~isnan(md2.mesh.lowervertex));
393 md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]394
[13692]395 md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
396 pos=find(~isnan(md2.mesh.upperelements));
397 md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]398
[13692]399 md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
400 pos=find(~isnan(md2.mesh.lowerelements));
401 md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
402 end
[13005]403
[13692]404 %Initial 2d mesh
[17558]405 if isa(md1.mesh,'mesh3dprisms'),
[13692]406 flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
407 pos_elem_2d=find(flag_elem_2d);
408 flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
409 pos_node_2d=find(flag_node_2d);
[13005]410
[13692]411 md2.mesh.numberofelements2d=length(pos_elem_2d);
412 md2.mesh.numberofvertices2d=length(pos_node_2d);
413 md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
414 md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
415 md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
416 md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]417
[13692]418 md2.mesh.x2d=md1.mesh.x(pos_node_2d);
419 md2.mesh.y2d=md1.mesh.y(pos_node_2d);
420 end
[13005]421
[13692]422 %Edges
[17563]423 if(strcmp(meshtype(md.mesh),'2Dhorizontal')),
424 if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
425 %renumber first two columns
426 pos=find(md2.mesh.edges(:,4)~=-1);
427 md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
428 md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
429 md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
430 md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
431 %remove edges when the 2 vertices are not in the domain.
432 md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
433 %Replace all zeros by -1 in the last two columns
434 pos=find(md2.mesh.edges(:,3)==0);
435 md2.mesh.edges(pos,3)=-1;
436 pos=find(md2.mesh.edges(:,4)==0);
437 md2.mesh.edges(pos,4)=-1;
438 %Invert -1 on the third column with last column (Also invert first two columns!!)
439 pos=find(md2.mesh.edges(:,3)==-1);
440 md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
441 md2.mesh.edges(pos,4)=-1;
442 values=md2.mesh.edges(pos,2);
443 md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
444 md2.mesh.edges(pos,1)=values;
445 %Finally remove edges that do not belong to any element
446 pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
447 md2.mesh.edges(pos,:)=[];
448 end
[13692]449 end
[13005]450
[13692]451 %Penalties
[15771]452 if ~isnan(md2.stressbalance.vertex_pairing),
453 for i=1:size(md1.stressbalance.vertex_pairing,1);
454 md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]455 end
[15771]456 md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]457 end
[15767]458 if ~isnan(md2.masstransport.vertex_pairing),
459 for i=1:size(md1.masstransport.vertex_pairing,1);
460 md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]461 end
[15767]462 md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]463 end
[13005]464
[13692]465 %recreate segments
[17558]466 if isa(md1.mesh,'mesh2d'),
[13692]467 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
468 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
469 md2.mesh.segments=contourenvelope(md2);
470 md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
471 else
472 %First do the connectivity for the contourenvelope in 2d
473 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
474 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
475 md2.mesh.segments=contourenvelope(md2);
476 md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
477 md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
478 %Then do it for 3d as usual
479 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
480 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
481 end
[13005]482
[13692]483 %Boundary conditions: Dirichlets on new boundary
484 %Catch the elements that have not been extracted
485 orphans_elem=find(~flag_elem);
486 orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
487 %Figure out which node are on the boundary between md2 and md1
488 nodestoflag1=intersect(orphans_node,pos_node);
489 nodestoflag2=Pnode(nodestoflag1);
[15771]490 if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
[13692]491 if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]492 md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
493 md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]494 else
[15771]495 md2.stressbalance.spcvx(nodestoflag2)=NaN;
496 md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]497 disp(' ')
498 disp('!! extract warning: spc values should be checked !!')
499 disp(' ')
500 end
501 %put 0 for vz
[15771]502 md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]503 end
504 if ~isnan(md1.thermal.spctemperature),
505 md2.thermal.spctemperature(nodestoflag2,1)=1;
506 end
[13005]507
[13692]508 %Results fields
509 if isstruct(md1.results),
510 md2.results=struct();
511 solutionfields=fields(md1.results);
512 for i=1:length(solutionfields),
[14230]513 if isstruct(md1.results.(solutionfields{i}))
514 %get subfields
515 solutionsubfields=fields(md1.results.(solutionfields{i}));
516 for j=1:length(solutionsubfields),
517 field=md1.results.(solutionfields{i}).(solutionsubfields{j});
518 if length(field)==numberofvertices1,
519 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
520 elseif length(field)==numberofelements1,
521 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
522 else
523 md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
524 end
525 end
526 else
527 field=md1.results.(solutionfields{i});
[13692]528 if length(field)==numberofvertices1,
[14230]529 md2.results.(solutionfields{i})=field(pos_node);
[13692]530 elseif length(field)==numberofelements1,
[14230]531 md2.results.(solutionfields{i})=field(pos_elem);
[13692]532 else
[14230]533 md2.results.(solutionfields{i})=field;
[13692]534 end
535 end
536 end
537 end
[13005]538
[13692]539 %Keep track of pos_node and pos_elem
540 md2.mesh.extractedvertices=pos_node;
541 md2.mesh.extractedelements=pos_elem;
542 end % }}}
543 function md = extrude(md,varargin) % {{{
544 %EXTRUDE - vertically extrude a 2d mesh
545 %
546 % vertically extrude a 2d mesh and create corresponding 3d mesh.
547 % The vertical distribution can:
548 % - follow a polynomial law
549 % - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
550 % - be discribed by a list of coefficients (between 0 and 1)
551 %
552 %
553 % Usage:
554 % md=extrude(md,numlayers,extrusionexponent);
555 % md=extrude(md,numlayers,lowerexponent,upperexponent);
556 % md=extrude(md,listofcoefficients);
557 %
558 % Example:
559 % md=extrude(md,8,3);
560 % md=extrude(md,8,3,2);
561 % md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
562 %
563 % See also: MODELEXTRACT, COLLAPSE
[13005]564
[13692]565 %some checks on list of arguments
566 if ((nargin>4) | (nargin<2) | (nargout~=1)),
567 help extrude;
568 error('extrude error message');
569 end
[13005]570
[13692]571 %Extrude the mesh
572 if nargin==2, %list of coefficients
573 clist=varargin{1};
574 if any(clist<0) | any(clist>1),
575 error('extrusioncoefficients must be between 0 and 1');
576 end
577 extrusionlist=sort(unique([clist(:);0;1]));
578 numlayers=length(extrusionlist);
579 elseif nargin==3, %one polynomial law
580 if varargin{2}<=0,
581 help extrude;
582 error('extrusionexponent must be >=0');
583 end
584 numlayers=varargin{1};
585 extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
586 elseif nargin==4, %two polynomial laws
587 numlayers=varargin{1};
588 lowerexp=varargin{2};
589 upperexp=varargin{3};
[13005]590
[13692]591 if varargin{2}<=0 | varargin{3}<=0,
592 help extrude;
593 error('lower and upper extrusionexponents must be >=0');
594 end
[13005]595
[13692]596 lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
597 upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
598 extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]599
[13692]600 end
[13005]601
[13692]602 if numlayers<2,
603 error('number of layers should be at least 2');
604 end
[17558]605 if strcmp(md.mesh.meshtype(),'3D')
[13692]606 error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
607 end
[13005]608
[13692]609 %Initialize with the 2d mesh
[17558]610 mesh2d = md.mesh;
611 md.mesh=mesh3dprisms();
612 md.mesh.x = mesh2d.x;
613 md.mesh.y = mesh2d.y;
614 md.mesh.elements = mesh2d.elements;
615 md.mesh.numberofelements = mesh2d.numberofelements;
616 md.mesh.numberofvertices = mesh2d.numberofvertices;
617
618 md.mesh.lat = mesh2d.lat;
619 md.mesh.long = mesh2d.long;
620 md.mesh.hemisphere = mesh2d.hemisphere;
621
622 md.mesh.vertexonboundary = mesh2d.vertexonboundary;
623 md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
624 md.mesh.elementconnectivity = mesh2d.elementconnectivity;
625 md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
626
627 md.mesh.extractedvertices = mesh2d.extractedvertices;
628 md.mesh.extractedelements = mesh2d.extractedelements;
629
[13692]630 x3d=[];
631 y3d=[];
632 z3d=[]; %the lower node is on the bed
633 thickness3d=md.geometry.thickness; %thickness and bed for these nodes
634 bed3d=md.geometry.bed;
[13005]635
[13692]636 %Create the new layers
637 for i=1:numlayers,
638 x3d=[x3d; md.mesh.x];
639 y3d=[y3d; md.mesh.y];
640 %nodes are distributed between bed and surface accordingly to the given exponent
641 z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
642 end
643 number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]644
[13692]645 %Extrude elements
646 elements3d=[];
647 for i=1:numlayers-1,
648 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
649 end
650 number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]651
[13692]652 %Keep a trace of lower and upper nodes
653 mesh.lowervertex=NaN*ones(number_nodes3d,1);
654 mesh.uppervertex=NaN*ones(number_nodes3d,1);
655 mesh.lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
656 mesh.uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
657 md.mesh.lowervertex=mesh.lowervertex;
658 md.mesh.uppervertex=mesh.uppervertex;
[13005]659
[13692]660 %same for lower and upper elements
661 mesh.lowerelements=NaN*ones(number_el3d,1);
662 mesh.upperelements=NaN*ones(number_el3d,1);
663 mesh.lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
664 mesh.upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
665 md.mesh.lowerelements=mesh.lowerelements;
666 md.mesh.upperelements=mesh.upperelements;
[13005]667
[13692]668 %Save old mesh
669 md.mesh.x2d=md.mesh.x;
670 md.mesh.y2d=md.mesh.y;
671 md.mesh.elements2d=md.mesh.elements;
672 md.mesh.numberofelements2d=md.mesh.numberofelements;
673 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]674
[13692]675 %Build global 3d mesh
676 md.mesh.elements=elements3d;
677 md.mesh.x=x3d;
678 md.mesh.y=y3d;
679 md.mesh.z=z3d;
680 md.mesh.numberofelements=number_el3d;
681 md.mesh.numberofvertices=number_nodes3d;
682 md.mesh.numberoflayers=numlayers;
[13005]683
[13692]684 %Ok, now deal with the other fields from the 2d mesh:
[13005]685
[13692]686 %lat long
687 md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
688 md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[13005]689
[13692]690 %drag coefficient is limited to nodes that are on the bedrock.
691 md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1);
[13005]692
[13692]693 %p and q (same deal, except for element that are on the bedrock: )
694 md.friction.p=project3d(md,'vector',md.friction.p,'type','element');
695 md.friction.q=project3d(md,'vector',md.friction.q,'type','element');
[13005]696
[13692]697 %observations
698 md.inversion.vx_obs=project3d(md,'vector',md.inversion.vx_obs,'type','node');
699 md.inversion.vy_obs=project3d(md,'vector',md.inversion.vy_obs,'type','node');
700 md.inversion.vel_obs=project3d(md,'vector',md.inversion.vel_obs,'type','node');
[16577]701 md.inversion.thickness_obs=project3d(md,'vector',md.inversion.thickness_obs,'type','node');
[17079]702 md.surfaceforcings = extrude(md.surfaceforcings,md);
[13692]703 md.balancethickness.thickening_rate=project3d(md,'vector',md.balancethickness.thickening_rate,'type','node');
[13005]704
[13692]705 %results
706 if ~isnan(md.initialization.vx),md.initialization.vx=project3d(md,'vector',md.initialization.vx,'type','node');end;
707 if ~isnan(md.initialization.vy),md.initialization.vy=project3d(md,'vector',md.initialization.vy,'type','node');end;
708 if ~isnan(md.initialization.vz),md.initialization.vz=project3d(md,'vector',md.initialization.vz,'type','node');end;
709 if ~isnan(md.initialization.vel),md.initialization.vel=project3d(md,'vector',md.initialization.vel,'type','node');end;
710 if ~isnan(md.initialization.temperature),md.initialization.temperature=project3d(md,'vector',md.initialization.temperature,'type','node');end;
711 if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project3d(md,'vector',md.initialization.waterfraction,'type','node');end;
[16559]712 if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project3d(md,'vector',md.initialization.watercolumn,'type','node','layer',1);end;
713 if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project3d(md,'vector',md.initialization.sediment_head,'type','node','layer',1);end;
714 if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project3d(md,'vector',md.initialization.epl_head,'type','node','layer',1);end;
[17523]715 if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project3d(md,'vector',md.initialization.epl_thickness,'type','node','layer',1);end;
[13005]716
[13692]717 %bedinfo and surface info
718 md.mesh.elementonbed=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',1);
719 md.mesh.elementonsurface=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',md.mesh.numberoflayers-1);
720 md.mesh.vertexonbed=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
721 md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
[13005]722
[13692]723 %elementstype
724 if ~isnan(md.flowequation.element_equation)
725 oldelements_type=md.flowequation.element_equation;
726 md.flowequation.element_equation=zeros(number_el3d,1);
727 md.flowequation.element_equation=project3d(md,'vector',oldelements_type,'type','element');
728 end
[13005]729
[13692]730 %verticestype
731 if ~isnan(md.flowequation.vertex_equation)
732 oldvertices_type=md.flowequation.vertex_equation;
733 md.flowequation.vertex_equation=zeros(number_nodes3d,1);
734 md.flowequation.vertex_equation=project3d(md,'vector',oldvertices_type,'type','node');
735 end
[15564]736 md.flowequation.borderSSA=project3d(md,'vector',md.flowequation.borderSSA,'type','node');
737 md.flowequation.borderHO=project3d(md,'vector',md.flowequation.borderHO,'type','node');
738 md.flowequation.borderFS=project3d(md,'vector',md.flowequation.borderFS,'type','node');
[13005]739
[13692]740 %boundary conditions
[15771]741 md.stressbalance.spcvx=project3d(md,'vector',md.stressbalance.spcvx,'type','node');
742 md.stressbalance.spcvy=project3d(md,'vector',md.stressbalance.spcvy,'type','node');
743 md.stressbalance.spcvz=project3d(md,'vector',md.stressbalance.spcvz,'type','node');
[13692]744 md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',NaN);
[17562]745 if (length(md.initialization.temperature)==md.mesh.numberofvertices),
746 md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1);
747 if isprop(md.mesh,'vertexonsurface'),
748 pos=find(md.mesh.vertexonsurface);
749 md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface
750 end
751 end
[15767]752 md.masstransport.spcthickness=project3d(md,'vector',md.masstransport.spcthickness,'type','node');
[17435]753 md.masstransport.calvingrate=project3d(md,'vector',md.masstransport.calvingrate,'type','node');
[13692]754 md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
[16190]755 md.damage.spcdamage=project3d(md,'vector',md.damage.spcdamage,'type','node');
[15771]756 md.stressbalance.referential=project3d(md,'vector',md.stressbalance.referential,'type','node');
757 md.stressbalance.loadingforce=project3d(md,'vector',md.stressbalance.loadingforce,'type','node');
[17422]758
759 % Hydrologydc variables
[16559]760 if isa(md.hydrology,'hydrologydc');
761 md.hydrology.spcsediment_head=project3d(md,'vector',md.hydrology.spcsediment_head,'type','node','layer',1);
762 md.hydrology.spcepl_head=project3d(md,'vector',md.hydrology.spcepl_head,'type','node','layer',1);
[16861]763 md.hydrology.mask_eplactive_node=project3d(md,'vector',md.hydrology.mask_eplactive_node,'type','node','layer',1);
[17022]764 md.hydrology.sediment_transmitivity=project3d(md,'vector',md.hydrology.sediment_transmitivity,'type','node','layer',1);
[17422]765 md.hydrology.basal_moulin_input=project3d(md,'vector',md.hydrology.basal_moulin_input,'type','node','layer',1);
[16559]766 end
[13005]767
[13692]768 %connectivity
769 md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
770 md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
771 for i=2:numlayers-1,
772 md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
773 =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
774 end
775 md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13005]776
[13692]777 %materials
778 md.materials.rheology_B=project3d(md,'vector',md.materials.rheology_B,'type','node');
779 md.materials.rheology_n=project3d(md,'vector',md.materials.rheology_n,'type','element');
[16160]780
781 %damage
782 md.damage.D=project3d(md,'vector',md.damage.D,'type','node');
[13005]783
[13692]784 %parameters
785 md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
786 md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
[14901]787 md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node');
[14724]788 md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node');
[13692]789 md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
790 md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
791 md.geometry.bathymetry=project3d(md,'vector',md.geometry.bathymetry,'type','node');
792 md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
[15957]793 md.mask.groundedice_levelset=project3d(md,'vector',md.mask.groundedice_levelset,'type','node');
[15943]794 md.mask.ice_levelset=project3d(md,'vector',md.mask.ice_levelset,'type','node');
[13692]795 if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end;
796 if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end;
797 if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end;
798 if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end
[13005]799
[13692]800 %Put lithostatic pressure if there is an existing pressure
801 if ~isnan(md.initialization.pressure),
802 md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z);
803 end
[13005]804
[13692]805 %special for thermal modeling:
806 md.basalforcings.melting_rate=project3d(md,'vector',md.basalforcings.melting_rate,'type','node','layer',1);
807 if ~isnan(md.basalforcings.geothermalflux)
808 md.basalforcings.geothermalflux=project3d(md,'vector',md.basalforcings.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux
809 end
[13005]810
[13692]811 %increase connectivity if less than 25:
812 if md.mesh.average_vertex_connectivity<=25,
813 md.mesh.average_vertex_connectivity=100;
814 end
[13005]815 end % }}}
[13692]816 function md = structtomodel(md,structmd) % {{{
[8952]817
[13692]818 if ~isstruct(structmd) error('input model is not a structure'); end
[8952]819
[13692]820 %loaded model is a struct, initialize output and recover all fields
821 md = structtoobj(model,structmd);
[8952]822
[13692]823 %Old field now classes
824 if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
825 if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]826
[13692]827 %Field name change
828 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
829 if isfield(structmd,'p'), md.friction.p=structmd.p; end
830 if isfield(structmd,'q'), md.friction.q=structmd.p; end
831 if isfield(structmd,'melting'), md.basalforcings.melting_rate=structmd.melting; end
832 if isfield(structmd,'melting_rate'), md.basalforcings.melting_rate=structmd.melting_rate; end
833 if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
834 if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
835 if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
836 if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
837 if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
838 if isfield(structmd,'gridonbed'), md.mesh.vertexonbed=structmd.gridonbed; end
839 if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
840 if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
841 if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]842 if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]843 if isfield(structmd,'g'), md.constants.g=structmd.g; end
844 if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
845 if isfield(structmd,'surface_mass_balance'), md.surfaceforcings.mass_balance=structmd.surface_mass_balance; end
846 if isfield(structmd,'basal_melting_rate'), md.basalforcings.melting_rate=structmd.basal_melting_rate; end
847 if isfield(structmd,'basal_melting_rate_correction'), md.basalforcings.melting_rate_correction=structmd.basal_melting_rate_correction; end
848 if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
849 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
850 if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
851 if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
852 if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
853 if isfield(structmd,'riftproperties'), %old implementation
854 md.rifts=rifts();
855 md.rifts.riftproperties=structmd.riftproperties;
856 md.rifts.riftstruct=structmd.rifts;
857 md.rifts.riftproperties=structmd.riftinfo;
858 end
859 if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
860 if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
861 if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
862 if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
863 if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
864 if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
865 if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
866 if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
867 if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
868 if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
869 if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
870 if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
871 if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
872 if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
873 if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
874 if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
875 if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
876 if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
877 if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
878 if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
879 if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
880 if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]881 if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
882 if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
883 if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
884 if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
885 if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]886 if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
887 if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
888 if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
889 if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]890 if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]891 if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
892 if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
893 if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]894 if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
895 if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]896 if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
897 if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
898 if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
899 if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]900 if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]901 if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]902 if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
903 if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
904 if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
905 if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
906 if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
907 if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
908 if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
909 if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
910 if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
911 if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
912 if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
913 if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
914 if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
915 if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
916 if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
917 if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
918 if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
919 if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
920 if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
921 if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
922 if isfield(structmd,'bed'), md.geometry.bed=structmd.bed; end
923 if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
924 if isfield(structmd,'bathymetry'), md.geometry.bathymetry=structmd.bathymetry; end
925 if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
926 if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
927 if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
928 if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
929 if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
930 if isfield(structmd,'hemisphere'), md.mesh.hemisphere=structmd.hemisphere; end
931 if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
932 if isfield(structmd,'long'), md.mesh.long=structmd.long; end
933 if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
934 if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
935 if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
936 if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
937 if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
938 if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
939 if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
940 if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
941 if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
942 if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
943 if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
944 if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
945 if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
946 if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
947 if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
948 if isfield(structmd,'elementonbed'), md.mesh.elementonbed=structmd.elementonbed; end
949 if isfield(structmd,'elementonsurface'), md.mesh.elementonsurface=structmd.elementonsurface; end
950 if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
951 if isfield(structmd,'nodeonbed'), md.mesh.vertexonbed=structmd.nodeonbed; end
952 if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
953 if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
954 if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
955 if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]956 if isfield(structmd,'edges'),
957 md.mesh.edges=structmd.edges;
958 md.mesh.edges(isnan(md.mesh.edges))=-1;
959 end
[13692]960 if isfield(structmd,'y'), md.mesh.y=structmd.y; end
961 if isfield(structmd,'x'), md.mesh.x=structmd.x; end
962 if isfield(structmd,'z'), md.mesh.z=structmd.z; end
963 if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
[15771]964 if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]965 if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
966 if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]967
[13692]968 if isnumeric(md.verbose),
969 md.verbose=verbose;
970 end
[15768]971
[13692]972 if isfield(structmd,'spcvelocity'),
[15771]973 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
974 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
975 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
976 pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
977 pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
978 pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]979 end
980 if isfield(structmd,'spcvx'),
[15771]981 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
982 pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]983 end
984 if isfield(structmd,'spcvy'),
[15771]985 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
986 pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]987 end
988 if isfield(structmd,'spcvz'),
[15771]989 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
990 pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]991 end
[14620]992 if isfield(structmd,'pressureload'),
993 if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]994 pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
995 pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
996 pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]997 end
[13692]998 end
999 if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
1000 pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
1001 pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
1002 pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
1003 pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
1004 pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
1005 pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
1006 pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
1007 pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
1008 end
1009 if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
1010 pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
1011 pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
1012 pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
1013 pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
1014 pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
1015 pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
1016 pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
1017 pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
1018 end
1019 if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
1020 if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
1021 if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1022 if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1023 end
1024 if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1025 if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1026 if (structmd.groundingline_migration==273), md.groundingline.migration='AgressiveMigration'; end
1027 if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1028 end
1029 if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1030 if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1031 if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1032 if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1033 end
1034 if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1035 pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1036 pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1037 pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1038 pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1039 pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1040 pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1041 pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1042 pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1043 pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1044 end
[11659]1045
[13692]1046 if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1047 md.thermal.stabilization=2;
[15767]1048 md.masstransport.stabilization=1;
[13692]1049 md.balancethickness.stabilization=1;
1050 end
[15767]1051 if isnumeric(md.masstransport.hydrostatic_adjustment)
1052 if md.masstransport.hydrostatic_adjustment==269,
1053 md.masstransport.hydrostatic_adjustment='Incremental';
[13692]1054 else
[15767]1055 md.masstransport.hydrostatic_adjustment='Absolute';
[13692]1056 end
1057 end
[8952]1058
[13692]1059 %New fields
1060 if ~isfield(structmd,'upperelements');
1061 md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1062 md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1063 end
1064 if ~isfield(structmd,'lowerelements');
1065 md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1066 md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1067 end
1068 if ~isfield(structmd,'diagnostic_ref');
[15771]1069 md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]1070 end
[14529]1071 if ~isfield(structmd,'loadingforce');
[15771]1072 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]1073 end
[15768]1074
1075 %2013 August 9
1076 if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1077 disp('Recovering old prognostic class');
1078 md.masstransport=masstransport(structmd.prognostic);
1079 end
[15771]1080 %2013 August 9
[15775]1081 if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') || isa(structmd.diagnostic,'stressbalance')),
[15771]1082 disp('Recovering old diagnostic class');
[15775]1083 md.stressbalance=stressbalance(structmd.diagnostic);
[15771]1084 end
[13692]1085 end% }}}
1086 function md = setdefaultparameters(md) % {{{
[8926]1087
[13692]1088 %initialize subclasses
[17558]1089 md.mesh = mesh2d();
[13692]1090 md.mask = mask();
1091 md.constants = constants();
1092 md.geometry = geometry();
1093 md.initialization = initialization();
[17079]1094 md.surfaceforcings = SMB();
[13692]1095 md.basalforcings = basalforcings();
1096 md.friction = friction();
1097 md.rifts = rifts();
1098 md.timestepping = timestepping();
1099 md.groundingline = groundingline();
1100 md.materials = matice();
[16160]1101 md.damage = damage();
[13692]1102 md.flowequation = flowequation();
1103 md.debug = debug();
[14558]1104 md.verbose = verbose();
[13692]1105 md.settings = settings();
[14621]1106 md.toolkits = toolkits();
[13692]1107 md.cluster = generic();
1108 md.balancethickness = balancethickness();
[17079]1109 md.stressbalance = stressbalance();
[14555]1110 md.hydrology = hydrologyshreve();
[17079]1111 md.masstransport = masstransport();
[13692]1112 md.thermal = thermal();
1113 md.steadystate = steadystate();
1114 md.transient = transient();
[14724]1115 md.gia = gia();
[13692]1116 md.autodiff = autodiff();
1117 md.flaim = flaim();
1118 md.inversion = inversion();
1119 md.qmu = qmu();
1120 md.radaroverlay = radaroverlay();
1121 md.results = struct();
[16388]1122 md.outputdefinition = outputdefinition();
[13692]1123 md.miscellaneous = miscellaneous();
1124 md.private = private();
1125 end
1126 %}}}
[17483]1127 function md = tetras(md,varargin) % {{{
1128 %TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1129 %
1130 % Usage:
1131 % md=tetra(md)
1132
1133 if ~isa(md.mesh,'mesh3dprisms')
1134 error('mesh is not a 3d prismatic mesh');
1135 end
1136
1137 %Initialize tetra mesh
1138 md.mesh=mesh3dtetras(md.mesh);
1139
1140 %Split in 3 tetras
1141 subelement1 = [1 2 3 5];
1142 subelement2 = [4 6 5 1];
1143 subelement3 = [5 6 3 1];
1144 elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
1145 pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1146
1147 md.mesh.elements=elements;
1148 md.mesh.numberofelements=size(elements,1);
1149
1150 %p and q (same deal, except for element that are on the bedrock: )
1151 md.friction.p=md.friction.p(pos_elements);
1152 md.friction.q=md.friction.q(pos_elements);
1153
1154 %elementstype
1155 if ~isnan(md.flowequation.element_equation)
1156 oldelements_type=md.flowequation.element_equation;
1157 md.flowequation.element_equation=zeros(number_el3d,1);
1158 md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1159 end
1160
1161 %connectivity
1162 md.mesh.elementconnectivity=NaN;
1163
1164 %materials
1165 md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1166
1167 %increase connectivity if less than 25:
1168 if md.mesh.average_vertex_connectivity<=25,
1169 md.mesh.average_vertex_connectivity=100;
1170 end
1171 end % }}}
[13692]1172 function disp(obj) % {{{
1173 disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(obj.mesh) ']'],'mesh properties'));
1174 disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(obj.mask) ']'],'defines grounded and floating elements'));
1175 disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(obj.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1176 disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(obj.constants) ']'],'physical constants'));
1177 disp(sprintf('%19s: %-22s -- %s','surfaceforcings' ,['[1x1 ' class(obj.surfaceforcings) ']'],'surface forcings'));
1178 disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(obj.basalforcings) ']'],'bed forcings'));
1179 disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(obj.materials) ']'],'material properties'));
[17367]1180 disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(obj.damage) ']'],'parameters for damage evolution solution'));
[13692]1181 disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(obj.friction) ']'],'basal friction/drag properties'));
1182 disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(obj.flowequation) ']'],'flow equations'));
1183 disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(obj.timestepping) ']'],'time stepping for transient models'));
1184 disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(obj.initialization) ']'],'initial guess/state'));
1185 disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(obj.rifts) ']'],'rifts properties'));
1186 disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(obj.debug) ']'],'debugging tools (valgrind, gprof)'));
1187 disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
1188 disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
[14621]1189 disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(obj.toolkits) ']'],'PETSc options for each solution'));
[13692]1190 disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
1191 disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
[15771]1192 disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(obj.stressbalance) ']'],'parameters for stressbalance solution'));
[13692]1193 disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(obj.groundingline) ']'],'parameters for groundingline solution'));
1194 disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(obj.hydrology) ']'],'parameters for hydrology solution'));
[15767]1195 disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(obj.masstransport) ']'],'parameters for masstransport solution'));
[13692]1196 disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(obj.thermal) ']'],'parameters for thermal solution'));
1197 disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
1198 disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
[14724]1199 disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(obj.gia) ']'],'parameters for gia solution'));
[13692]1200 disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
1201 disp(sprintf('%19s: %-22s -- %s','flaim' ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
1202 disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(obj.inversion) ']'],'parameters for inverse methods'));
1203 disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(obj.qmu) ']'],'dakota properties'));
[16388]1204 disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(obj.outputdefinition) ']'],'output definition'));
[13692]1205 disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(obj.results) ']'],'model results'));
1206 disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(obj.radaroverlay) ']'],'radar image for plot overlay'));
1207 disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields'));
1208 end % }}}
[14307]1209 function memory(obj) % {{{
[15106]1210
[14611]1211 disp(sprintf('\nMemory imprint:\n'));
[14307]1212
[14603]1213 fields=properties('model');
1214 mem=0;
[15106]1215
[14603]1216 for i=1:length(fields),
1217 field=obj.(fields{i});
1218 s=whos('field');
1219 mem=mem+s.bytes/1e6;
[14611]1220 disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]1221 end
[14603]1222 disp(sprintf('%19s--%10s','--------------','--------------'));
1223 disp(sprintf('%19s: %g Mb','Total',mem));
[14307]1224 end % }}}
[14603]1225 function netcdf(obj,filename) % {{{
1226 %NETCDF - save model as netcdf
1227 %
1228 % Usage:
1229 % netcdf(md,filename)
1230 %
1231 % Example:
1232 % netcdf(md,'model.nc');
1233
1234 disp('Saving model as NetCDF');
1235 %1. Create NetCDF file
1236 ncid=netcdf.create(filename,'CLOBBER');
1237 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[14611]1238 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' obj.miscellaneous.name ')']);
[14603]1239 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1240 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1241
[14611]1242 %Preallocate variable id, needed to write variables in netcdf file
[14631]1243 var_id=zeros(1000,1);%preallocate
[14609]1244
1245 for step=1:2,
1246 counter=0;
[14612]1247 [var_id,counter]=structtonc(ncid,'md',obj,0,var_id,counter,step);
[14609]1248 if step==1, netcdf.endDef(ncid); end
[14603]1249 end
[14611]1250
[14631]1251 if counter>1000,
1252 warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]1253 end
1254
1255 netcdf.close(ncid)
[14603]1256 end % }}}
[14405]1257 function xylim(obj) % {{{
1258
1259 xlim([min(obj.mesh.x) max(obj.mesh.x)]);
1260 ylim([min(obj.mesh.y) max(obj.mesh.y)])
1261 end % }}}
[15316]1262 function md=upload(md) % {{{
1263 %the goal of this routine is to upload the model onto a server, and to empty it.
1264 %So first, save the model with a unique name and upload the file to the server:
1265 random_part=fix(rand(1)*10000);
1266 id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1267 eval(['save ' id ' md']);
1268
1269 %Now, upload the file:
1270 issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1271
1272 %Now, empty this model of everything except settings, and record name of file we just uploaded!
1273 settings_back=md.settings;
1274 md=model();
1275 md.settings=settings_back;
1276 md.settings.upload_filename=id;
1277
1278 %get locally rid of file that was uploaded
1279 eval(['delete ' id]);
1280
1281 end % }}}
1282 function md=download(md) % {{{
[15643]1283
[15316]1284 %the goal of this routine is to download the internals of the current model from a server, because
1285 %this model is empty, except for the settings which tell us where to go and find this model!
[15643]1286
[15316]1287 %Download the file:
1288 issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1289
1290 name=md.settings.upload_filename;
1291
1292 %Now, load this model:
1293 md=loadmodel(md.settings.upload_filename);
1294
1295 %get locally rid of file that was downloaded
1296 eval(['delete ' name]);
1297
1298 end % }}}
[13692]1299 end
[8926]1300 end
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