source: issm/trunk-jpl/src/m/classes/model.m@ 17435

Last change on this file since 17435 was 17435, checked in by jbondzio, 11 years ago

ADD: extrusion of masstransport.calvingrate
File size: 59.9 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
[13692]113 end% }}}
114 end
115 methods
116 function md = model(varargin) % {{{
[8926]117
[13692]118 switch nargin
119 case 0
120 md=setdefaultparameters(md);
121 otherwise
122 error('model constructor error message: 0 of 1 argument only in input.');
123 end
124 end
125 %}}}
126 function md = checkmessage(md,string) % {{{
127 if(nargout~=1) error('wrong usage, model must be an output'); end
128 disp(['model not consistent: ' string]);
129 md.private.isconsistent=false;
130 end
131 %}}}
132 function md = collapse(md)% {{{
133 %COLLAPSE - collapses a 3d mesh into a 2d mesh
134 %
135 % This routine collapses a 3d model into a 2d model
136 % and collapses all the fileds of the 3d model by
137 % taking their depth-averaged values
138 %
139 % Usage:
140 % md=collapse(md)
141 %
142 % See also: EXTRUDE, MODELEXTRACT
[13005]143
[13692]144 %Check that the model is really a 3d model
145 if ~md.mesh.dimension==3,
146 error('collapse error message: only 3d mesh can be collapsed')
147 end
[13005]148
[13692]149 %Start with changing alle the fields from the 3d mesh
[13005]150
[13692]151 %drag is limited to nodes that are on the bedrock.
152 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
[13005]153
[13692]154 %p and q (same deal, except for element that are on the bedrock: )
155 md.friction.p=project2d(md,md.friction.p,1);
156 md.friction.q=project2d(md,md.friction.q,1);
[13005]157
[13692]158 %observations
159 if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
160 if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
161 if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
162 if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
163 if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
164 if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
165 if ~isnan(md.surfaceforcings.mass_balance),
166 md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers);
167 end;
168 if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;
[13005]169
[13692]170 %results
171 if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
172 if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
173 if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
174 if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
175 if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[13005]176
[15021]177 %gia
178 if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
179 if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
180
[13692]181 %bedinfo and surface info
182 md.mesh.elementonbed=ones(md.mesh.numberofelements2d,1);
183 md.mesh.elementonsurface=ones(md.mesh.numberofelements2d,1);
184 md.mesh.vertexonbed=ones(md.mesh.numberofvertices2d,1);
185 md.mesh.vertexonsurface=ones(md.mesh.numberofvertices2d,1);
[13005]186
[13692]187 %elementstype
188 if ~isnan(md.flowequation.element_equation)
189 md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
190 md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]191 md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
192 md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
193 md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]194 end
[13005]195
[13692]196 %boundary conditions
[15771]197 md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
198 md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
199 md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
200 md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
201 md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[15767]202 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
[16344]203 md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers)
[13692]204 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]205
[13692]206 %materials
207 md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
208 md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]209
210 %damage:
211 md.damage.D=DepthAverage(md,md.damage.D);
[13005]212
[13692]213 %special for thermal modeling:
214 md.basalforcings.melting_rate=project2d(md,md.basalforcings.melting_rate,1);
215 md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]216
[13692]217 %update of connectivity matrix
218 md.mesh.average_vertex_connectivity=25;
[13005]219
[13692]220 %Collapse the mesh
221 nodes2d=md.mesh.numberofvertices2d;
222 elements2d=md.mesh.numberofelements2d;
[13005]223
[13692]224 %parameters
225 md.geometry.surface=project2d(md,md.geometry.surface,1);
226 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
227 md.geometry.bed=project2d(md,md.geometry.bed,1);
228 md.geometry.bathymetry=project2d(md,md.geometry.bathymetry,1);
229 md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
230 md.mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
[15943]231 md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
232 md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
[13005]233
[13692]234 %lat long
235 if numel(md.mesh.lat) ==md.mesh.numberofvertices, md.mesh.lat=project2d(md,md.mesh.lat,1); end
236 if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end
[13005]237
[13692]238 %Initialize with the 2d mesh
239 md.mesh.x=md.mesh.x2d;
240 md.mesh.y=md.mesh.y2d;
241 md.mesh.z=zeros(size(md.mesh.x2d));
242 md.mesh.numberofvertices=md.mesh.numberofvertices2d;
243 md.mesh.numberofelements=md.mesh.numberofelements2d;
244 md.mesh.elements=md.mesh.elements2d;
[13005]245
[13692]246 %Keep a trace of lower and upper nodes
247 md.mesh.lowervertex=NaN;
248 md.mesh.uppervertex=NaN;
249 md.mesh.lowerelements=NaN;
250 md.mesh.upperelements=NaN;
[13005]251
[13692]252 %Remove old mesh
253 md.mesh.x2d=NaN;
254 md.mesh.y2d=NaN;
255 md.mesh.elements2d=NaN;
256 md.mesh.numberofelements2d=md.mesh.numberofelements;
257 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
258 md.mesh.numberoflayers=0;
[13005]259
[13692]260 %Update mesh type
261 md.mesh.dimension=2;
262 end % }}}
263 function md2 = extract(md,area) % {{{
264 %extract - extract a model according to an Argus contour or flag list
265 %
266 % This routine extracts a submodel from a bigger model with respect to a given contour
267 % md must be followed by the corresponding exp file or flags list
268 % It can either be a domain file (argus type, .exp extension), or an array of element flags.
269 % If user wants every element outside the domain to be
[15564]270 % extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]271 % an empty string '' will be considered as an empty domain
272 % a string 'all' will be considered as the entire domain
273 %
274 % Usage:
275 % md2=extract(md,area);
276 %
277 % Examples:
278 % md2=extract(md,'Domain.exp');
279 %
280 % See also: EXTRUDE, COLLAPSE
[13005]281
[13692]282 %copy model
283 md1=md;
[13005]284
[13692]285 %some checks
286 if ((nargin~=2) | (nargout~=1)),
287 help extract
288 error('extract error message: bad usage');
289 end
[13005]290
[13692]291 %get elements that are inside area
292 flag_elem=FlagElements(md1,area);
293 if ~any(flag_elem),
294 error('extracted model is empty');
295 end
[13005]296
[13692]297 %kick out all elements with 3 dirichlets
298 spc_elem=find(~flag_elem);
299 spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
300 flag=ones(md1.mesh.numberofvertices,1);
301 flag(spc_node)=0;
302 pos=find(sum(flag(md1.mesh.elements),2)==0);
303 flag_elem(pos)=0;
[13005]304
[13692]305 %extracted elements and nodes lists
306 pos_elem=find(flag_elem);
307 pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]308
[13692]309 %keep track of some fields
310 numberofvertices1=md1.mesh.numberofvertices;
311 numberofelements1=md1.mesh.numberofelements;
312 numberofvertices2=length(pos_node);
313 numberofelements2=length(pos_elem);
314 flag_node=zeros(numberofvertices1,1);
315 flag_node(pos_node)=1;
[13005]316
[13692]317 %Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
318 Pelem=zeros(numberofelements1,1);
319 Pelem(pos_elem)=[1:numberofelements2]';
320 Pnode=zeros(numberofvertices1,1);
321 Pnode(pos_node)=[1:numberofvertices2]';
[13005]322
[13857]323 %renumber the elements (some nodes won't exist anymore)
[13692]324 elements_1=md1.mesh.elements;
325 elements_2=elements_1(pos_elem,:);
326 elements_2(:,1)=Pnode(elements_2(:,1));
327 elements_2(:,2)=Pnode(elements_2(:,2));
328 elements_2(:,3)=Pnode(elements_2(:,3));
329 if md1.mesh.dimension==3,
330 elements_2(:,4)=Pnode(elements_2(:,4));
331 elements_2(:,5)=Pnode(elements_2(:,5));
332 elements_2(:,6)=Pnode(elements_2(:,6));
333 end
[13005]334
[13857]335 %OK, now create the new model!
[13005]336
[13857]337 %take every field from model
[13692]338 md2=md1;
[13005]339
[13692]340 %automatically modify fields
[13005]341
[13692]342 %loop over model fields
343 model_fields=fields(md1);
344 for i=1:length(model_fields),
345 %get field
346 field=md1.(model_fields{i});
347 fieldsize=size(field);
348 if isobject(field), %recursive call
349 object_fields=fields(md1.(model_fields{i}));
350 for j=1:length(object_fields),
351 %get field
352 field=md1.(model_fields{i}).(object_fields{j});
353 fieldsize=size(field);
354 %size = number of nodes * n
355 if fieldsize(1)==numberofvertices1
356 md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
357 elseif (fieldsize(1)==numberofvertices1+1)
358 md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]359 %size = number of elements * n
[13692]360 elseif fieldsize(1)==numberofelements1
361 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
362 end
363 end
364 else
365 %size = number of nodes * n
366 if fieldsize(1)==numberofvertices1
367 md2.(model_fields{i})=field(pos_node,:);
368 elseif (fieldsize(1)==numberofvertices1+1)
369 md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]370 %size = number of elements * n
[13692]371 elseif fieldsize(1)==numberofelements1
372 md2.(model_fields{i})=field(pos_elem,:);
373 end
374 end
375 end
[13005]376
[13692]377 %modify some specific fields
[13005]378
[13692]379 %Mesh
380 md2.mesh.numberofelements=numberofelements2;
381 md2.mesh.numberofvertices=numberofvertices2;
382 md2.mesh.elements=elements_2;
[13005]383
[13692]384 %mesh.uppervertex mesh.lowervertex
385 if md1.mesh.dimension==3
386 md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
387 pos=find(~isnan(md2.mesh.uppervertex));
388 md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]389
[13692]390 md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
391 pos=find(~isnan(md2.mesh.lowervertex));
392 md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]393
[13692]394 md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
395 pos=find(~isnan(md2.mesh.upperelements));
396 md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]397
[13692]398 md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
399 pos=find(~isnan(md2.mesh.lowerelements));
400 md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
401 end
[13005]402
[13692]403 %Initial 2d mesh
404 if md1.mesh.dimension==3
405 flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
406 pos_elem_2d=find(flag_elem_2d);
407 flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
408 pos_node_2d=find(flag_node_2d);
[13005]409
[13692]410 md2.mesh.numberofelements2d=length(pos_elem_2d);
411 md2.mesh.numberofvertices2d=length(pos_node_2d);
412 md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
413 md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
414 md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
415 md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]416
[13692]417 md2.mesh.x2d=md1.mesh.x(pos_node_2d);
418 md2.mesh.y2d=md1.mesh.y(pos_node_2d);
419 end
[13005]420
[13692]421 %Edges
422 if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
423 %renumber first two columns
424 pos=find(md2.mesh.edges(:,4)~=-1);
[13857]425 md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
426 md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
[13692]427 md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
428 md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
429 %remove edges when the 2 vertices are not in the domain.
430 md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
[13857]431 %Replace all zeros by -1 in the last two columns
[13692]432 pos=find(md2.mesh.edges(:,3)==0);
433 md2.mesh.edges(pos,3)=-1;
434 pos=find(md2.mesh.edges(:,4)==0);
435 md2.mesh.edges(pos,4)=-1;
436 %Invert -1 on the third column with last column (Also invert first two columns!!)
437 pos=find(md2.mesh.edges(:,3)==-1);
438 md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
439 md2.mesh.edges(pos,4)=-1;
440 values=md2.mesh.edges(pos,2);
441 md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
442 md2.mesh.edges(pos,1)=values;
443 %Finally remove edges that do not belong to any element
444 pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
445 md2.mesh.edges(pos,:)=[];
446 end
[13005]447
[13692]448 %Penalties
[15771]449 if ~isnan(md2.stressbalance.vertex_pairing),
450 for i=1:size(md1.stressbalance.vertex_pairing,1);
451 md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]452 end
[15771]453 md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]454 end
[15767]455 if ~isnan(md2.masstransport.vertex_pairing),
456 for i=1:size(md1.masstransport.vertex_pairing,1);
457 md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]458 end
[15767]459 md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]460 end
[13005]461
[13692]462 %recreate segments
463 if md1.mesh.dimension==2
464 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
465 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
466 md2.mesh.segments=contourenvelope(md2);
467 md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
468 else
469 %First do the connectivity for the contourenvelope in 2d
470 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
471 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
472 md2.mesh.segments=contourenvelope(md2);
473 md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
474 md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
475 %Then do it for 3d as usual
476 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
477 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
478 end
[13005]479
[13692]480 %Boundary conditions: Dirichlets on new boundary
481 %Catch the elements that have not been extracted
482 orphans_elem=find(~flag_elem);
483 orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
484 %Figure out which node are on the boundary between md2 and md1
485 nodestoflag1=intersect(orphans_node,pos_node);
486 nodestoflag2=Pnode(nodestoflag1);
[15771]487 if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
[13692]488 if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]489 md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
490 md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]491 else
[15771]492 md2.stressbalance.spcvx(nodestoflag2)=NaN;
493 md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]494 disp(' ')
495 disp('!! extract warning: spc values should be checked !!')
496 disp(' ')
497 end
498 %put 0 for vz
[15771]499 md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]500 end
501 if ~isnan(md1.thermal.spctemperature),
502 md2.thermal.spctemperature(nodestoflag2,1)=1;
503 end
[13005]504
[13692]505 %Results fields
506 if isstruct(md1.results),
507 md2.results=struct();
508 solutionfields=fields(md1.results);
509 for i=1:length(solutionfields),
[14230]510 if isstruct(md1.results.(solutionfields{i}))
511 %get subfields
512 solutionsubfields=fields(md1.results.(solutionfields{i}));
513 for j=1:length(solutionsubfields),
514 field=md1.results.(solutionfields{i}).(solutionsubfields{j});
515 if length(field)==numberofvertices1,
516 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
517 elseif length(field)==numberofelements1,
518 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
519 else
520 md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
521 end
522 end
523 else
524 field=md1.results.(solutionfields{i});
[13692]525 if length(field)==numberofvertices1,
[14230]526 md2.results.(solutionfields{i})=field(pos_node);
[13692]527 elseif length(field)==numberofelements1,
[14230]528 md2.results.(solutionfields{i})=field(pos_elem);
[13692]529 else
[14230]530 md2.results.(solutionfields{i})=field;
[13692]531 end
532 end
533 end
534 end
[13005]535
[13692]536 %Keep track of pos_node and pos_elem
537 md2.mesh.extractedvertices=pos_node;
538 md2.mesh.extractedelements=pos_elem;
539 end % }}}
540 function md = extrude(md,varargin) % {{{
541 %EXTRUDE - vertically extrude a 2d mesh
542 %
543 % vertically extrude a 2d mesh and create corresponding 3d mesh.
544 % The vertical distribution can:
545 % - follow a polynomial law
546 % - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
547 % - be discribed by a list of coefficients (between 0 and 1)
548 %
549 %
550 % Usage:
551 % md=extrude(md,numlayers,extrusionexponent);
552 % md=extrude(md,numlayers,lowerexponent,upperexponent);
553 % md=extrude(md,listofcoefficients);
554 %
555 % Example:
556 % md=extrude(md,8,3);
557 % md=extrude(md,8,3,2);
558 % md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
559 %
560 % See also: MODELEXTRACT, COLLAPSE
[13005]561
[13692]562 %some checks on list of arguments
563 if ((nargin>4) | (nargin<2) | (nargout~=1)),
564 help extrude;
565 error('extrude error message');
566 end
[13005]567
[13692]568 %Extrude the mesh
569 if nargin==2, %list of coefficients
570 clist=varargin{1};
571 if any(clist<0) | any(clist>1),
572 error('extrusioncoefficients must be between 0 and 1');
573 end
574 extrusionlist=sort(unique([clist(:);0;1]));
575 numlayers=length(extrusionlist);
576 elseif nargin==3, %one polynomial law
577 if varargin{2}<=0,
578 help extrude;
579 error('extrusionexponent must be >=0');
580 end
581 numlayers=varargin{1};
582 extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
583 elseif nargin==4, %two polynomial laws
584 numlayers=varargin{1};
585 lowerexp=varargin{2};
586 upperexp=varargin{3};
[13005]587
[13692]588 if varargin{2}<=0 | varargin{3}<=0,
589 help extrude;
590 error('lower and upper extrusionexponents must be >=0');
591 end
[13005]592
[13692]593 lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
594 upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
595 extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]596
[13692]597 end
[13005]598
[13692]599 if numlayers<2,
600 error('number of layers should be at least 2');
601 end
602 if md.mesh.dimension==3,
603 error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
604 end
[13005]605
[13692]606 %Initialize with the 2d mesh
607 x3d=[];
608 y3d=[];
609 z3d=[]; %the lower node is on the bed
610 thickness3d=md.geometry.thickness; %thickness and bed for these nodes
611 bed3d=md.geometry.bed;
[13005]612
[13692]613 %Create the new layers
614 for i=1:numlayers,
615 x3d=[x3d; md.mesh.x];
616 y3d=[y3d; md.mesh.y];
617 %nodes are distributed between bed and surface accordingly to the given exponent
618 z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
619 end
620 number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]621
[13692]622 %Extrude elements
623 elements3d=[];
624 for i=1:numlayers-1,
625 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
626 end
627 number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]628
[13692]629 %Keep a trace of lower and upper nodes
630 mesh.lowervertex=NaN*ones(number_nodes3d,1);
631 mesh.uppervertex=NaN*ones(number_nodes3d,1);
632 mesh.lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
633 mesh.uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
634 md.mesh.lowervertex=mesh.lowervertex;
635 md.mesh.uppervertex=mesh.uppervertex;
[13005]636
[13692]637 %same for lower and upper elements
638 mesh.lowerelements=NaN*ones(number_el3d,1);
639 mesh.upperelements=NaN*ones(number_el3d,1);
640 mesh.lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
641 mesh.upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
642 md.mesh.lowerelements=mesh.lowerelements;
643 md.mesh.upperelements=mesh.upperelements;
[13005]644
[13692]645 %Save old mesh
646 md.mesh.x2d=md.mesh.x;
647 md.mesh.y2d=md.mesh.y;
648 md.mesh.elements2d=md.mesh.elements;
649 md.mesh.numberofelements2d=md.mesh.numberofelements;
650 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]651
[13692]652 %Update mesh type
653 md.mesh.dimension=3;
[13005]654
[13692]655 %Build global 3d mesh
656 md.mesh.elements=elements3d;
657 md.mesh.x=x3d;
658 md.mesh.y=y3d;
659 md.mesh.z=z3d;
660 md.mesh.numberofelements=number_el3d;
661 md.mesh.numberofvertices=number_nodes3d;
662 md.mesh.numberoflayers=numlayers;
[13005]663
[13692]664 %Ok, now deal with the other fields from the 2d mesh:
[13005]665
[13692]666 %lat long
667 md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
668 md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[13005]669
[13692]670 %drag coefficient is limited to nodes that are on the bedrock.
671 md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1);
[13005]672
[13692]673 %p and q (same deal, except for element that are on the bedrock: )
674 md.friction.p=project3d(md,'vector',md.friction.p,'type','element');
675 md.friction.q=project3d(md,'vector',md.friction.q,'type','element');
[13005]676
[13692]677 %observations
678 md.inversion.vx_obs=project3d(md,'vector',md.inversion.vx_obs,'type','node');
679 md.inversion.vy_obs=project3d(md,'vector',md.inversion.vy_obs,'type','node');
680 md.inversion.vel_obs=project3d(md,'vector',md.inversion.vel_obs,'type','node');
[16577]681 md.inversion.thickness_obs=project3d(md,'vector',md.inversion.thickness_obs,'type','node');
[17079]682 md.surfaceforcings = extrude(md.surfaceforcings,md);
[13692]683 md.balancethickness.thickening_rate=project3d(md,'vector',md.balancethickness.thickening_rate,'type','node');
[13005]684
[13692]685 %results
686 if ~isnan(md.initialization.vx),md.initialization.vx=project3d(md,'vector',md.initialization.vx,'type','node');end;
687 if ~isnan(md.initialization.vy),md.initialization.vy=project3d(md,'vector',md.initialization.vy,'type','node');end;
688 if ~isnan(md.initialization.vz),md.initialization.vz=project3d(md,'vector',md.initialization.vz,'type','node');end;
689 if ~isnan(md.initialization.vel),md.initialization.vel=project3d(md,'vector',md.initialization.vel,'type','node');end;
690 if ~isnan(md.initialization.temperature),md.initialization.temperature=project3d(md,'vector',md.initialization.temperature,'type','node');end;
691 if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project3d(md,'vector',md.initialization.waterfraction,'type','node');end;
[16559]692 if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project3d(md,'vector',md.initialization.watercolumn,'type','node','layer',1);end;
693 if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project3d(md,'vector',md.initialization.sediment_head,'type','node','layer',1);end;
694 if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project3d(md,'vector',md.initialization.epl_head,'type','node','layer',1);end;
[13005]695
[13692]696 %bedinfo and surface info
697 md.mesh.elementonbed=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',1);
698 md.mesh.elementonsurface=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',md.mesh.numberoflayers-1);
699 md.mesh.vertexonbed=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
700 md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
[13005]701
[13692]702 %elementstype
703 if ~isnan(md.flowequation.element_equation)
704 oldelements_type=md.flowequation.element_equation;
705 md.flowequation.element_equation=zeros(number_el3d,1);
706 md.flowequation.element_equation=project3d(md,'vector',oldelements_type,'type','element');
707 end
[13005]708
[13692]709 %verticestype
710 if ~isnan(md.flowequation.vertex_equation)
711 oldvertices_type=md.flowequation.vertex_equation;
712 md.flowequation.vertex_equation=zeros(number_nodes3d,1);
713 md.flowequation.vertex_equation=project3d(md,'vector',oldvertices_type,'type','node');
714 end
[15564]715 md.flowequation.borderSSA=project3d(md,'vector',md.flowequation.borderSSA,'type','node');
716 md.flowequation.borderHO=project3d(md,'vector',md.flowequation.borderHO,'type','node');
717 md.flowequation.borderFS=project3d(md,'vector',md.flowequation.borderFS,'type','node');
[13005]718
[13692]719 %boundary conditions
[15771]720 md.stressbalance.spcvx=project3d(md,'vector',md.stressbalance.spcvx,'type','node');
721 md.stressbalance.spcvy=project3d(md,'vector',md.stressbalance.spcvy,'type','node');
722 md.stressbalance.spcvz=project3d(md,'vector',md.stressbalance.spcvz,'type','node');
[13692]723 md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',NaN);
[15767]724 md.masstransport.spcthickness=project3d(md,'vector',md.masstransport.spcthickness,'type','node');
[17435]725 md.masstransport.calvingrate=project3d(md,'vector',md.masstransport.calvingrate,'type','node');
[13692]726 md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
[16190]727 md.damage.spcdamage=project3d(md,'vector',md.damage.spcdamage,'type','node');
[15771]728 md.stressbalance.referential=project3d(md,'vector',md.stressbalance.referential,'type','node');
729 md.stressbalance.loadingforce=project3d(md,'vector',md.stressbalance.loadingforce,'type','node');
[17422]730
731 % Hydrologydc variables
[16559]732 if isa(md.hydrology,'hydrologydc');
733 md.hydrology.spcsediment_head=project3d(md,'vector',md.hydrology.spcsediment_head,'type','node','layer',1);
734 md.hydrology.spcepl_head=project3d(md,'vector',md.hydrology.spcepl_head,'type','node','layer',1);
[16861]735 md.hydrology.mask_eplactive_node=project3d(md,'vector',md.hydrology.mask_eplactive_node,'type','node','layer',1);
[17022]736 md.hydrology.sediment_transmitivity=project3d(md,'vector',md.hydrology.sediment_transmitivity,'type','node','layer',1);
[17422]737 md.hydrology.basal_moulin_input=project3d(md,'vector',md.hydrology.basal_moulin_input,'type','node','layer',1);
[16559]738 end
[13005]739
[13692]740 %connectivity
741 md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
742 md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
743 for i=2:numlayers-1,
744 md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
745 =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
746 end
747 md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13005]748
[13692]749 %materials
750 md.materials.rheology_B=project3d(md,'vector',md.materials.rheology_B,'type','node');
751 md.materials.rheology_n=project3d(md,'vector',md.materials.rheology_n,'type','element');
[16160]752
753 %damage
754 md.damage.D=project3d(md,'vector',md.damage.D,'type','node');
[13005]755
[13692]756 %parameters
757 md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
758 md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
[14901]759 md.gia.mantle_viscosity=project3d(md,'vector',md.gia.mantle_viscosity,'type','node');
[14724]760 md.gia.lithosphere_thickness=project3d(md,'vector',md.gia.lithosphere_thickness,'type','node');
[13692]761 md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
762 md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
763 md.geometry.bathymetry=project3d(md,'vector',md.geometry.bathymetry,'type','node');
764 md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
[15957]765 md.mask.groundedice_levelset=project3d(md,'vector',md.mask.groundedice_levelset,'type','node');
[15943]766 md.mask.ice_levelset=project3d(md,'vector',md.mask.ice_levelset,'type','node');
[13692]767 if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end;
768 if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end;
769 if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end;
770 if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end
[13005]771
[13692]772 %Put lithostatic pressure if there is an existing pressure
773 if ~isnan(md.initialization.pressure),
774 md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z);
775 end
[13005]776
[13692]777 %special for thermal modeling:
778 md.basalforcings.melting_rate=project3d(md,'vector',md.basalforcings.melting_rate,'type','node','layer',1);
779 if ~isnan(md.basalforcings.geothermalflux)
780 md.basalforcings.geothermalflux=project3d(md,'vector',md.basalforcings.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux
781 end
[13005]782
[13692]783 %increase connectivity if less than 25:
784 if md.mesh.average_vertex_connectivity<=25,
785 md.mesh.average_vertex_connectivity=100;
786 end
[13005]787 end % }}}
[13692]788 function md = structtomodel(md,structmd) % {{{
[8952]789
[13692]790 if ~isstruct(structmd) error('input model is not a structure'); end
[8952]791
[13692]792 %loaded model is a struct, initialize output and recover all fields
793 md = structtoobj(model,structmd);
[8952]794
[13692]795 %Old field now classes
796 if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
797 if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]798
[13692]799 %Field name change
800 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
801 if isfield(structmd,'p'), md.friction.p=structmd.p; end
802 if isfield(structmd,'q'), md.friction.q=structmd.p; end
803 if isfield(structmd,'melting'), md.basalforcings.melting_rate=structmd.melting; end
804 if isfield(structmd,'melting_rate'), md.basalforcings.melting_rate=structmd.melting_rate; end
805 if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
806 if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
807 if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
808 if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
809 if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
810 if isfield(structmd,'gridonbed'), md.mesh.vertexonbed=structmd.gridonbed; end
811 if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
812 if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
813 if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]814 if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]815 if isfield(structmd,'g'), md.constants.g=structmd.g; end
816 if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
817 if isfield(structmd,'surface_mass_balance'), md.surfaceforcings.mass_balance=structmd.surface_mass_balance; end
818 if isfield(structmd,'basal_melting_rate'), md.basalforcings.melting_rate=structmd.basal_melting_rate; end
819 if isfield(structmd,'basal_melting_rate_correction'), md.basalforcings.melting_rate_correction=structmd.basal_melting_rate_correction; end
820 if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
821 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
822 if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
823 if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
824 if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
825 if isfield(structmd,'riftproperties'), %old implementation
826 md.rifts=rifts();
827 md.rifts.riftproperties=structmd.riftproperties;
828 md.rifts.riftstruct=structmd.rifts;
829 md.rifts.riftproperties=structmd.riftinfo;
830 end
831 if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
832 if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
833 if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
834 if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
835 if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
836 if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
837 if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
838 if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
839 if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
840 if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
841 if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
842 if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
843 if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
844 if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
845 if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
846 if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
847 if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
848 if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
849 if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
850 if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
851 if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
852 if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]853 if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
854 if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
855 if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
856 if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
857 if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]858 if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
859 if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
860 if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
861 if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]862 if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]863 if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
864 if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
865 if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]866 if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
867 if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]868 if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
869 if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
870 if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
871 if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]872 if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]873 if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]874 if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
875 if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
876 if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
877 if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
878 if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
879 if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
880 if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
881 if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
882 if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
883 if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
884 if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
885 if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
886 if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
887 if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
888 if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
889 if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
890 if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
891 if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
892 if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
893 if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
894 if isfield(structmd,'bed'), md.geometry.bed=structmd.bed; end
895 if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
896 if isfield(structmd,'bathymetry'), md.geometry.bathymetry=structmd.bathymetry; end
897 if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
898 if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
899 if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
900 if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
901 if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
902 if isfield(structmd,'hemisphere'), md.mesh.hemisphere=structmd.hemisphere; end
903 if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
904 if isfield(structmd,'long'), md.mesh.long=structmd.long; end
905 if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
906 if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
907 if isfield(structmd,'dim'), md.mesh.dimension=structmd.dim; end
908 if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
909 if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
910 if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
911 if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
912 if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
913 if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
914 if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
915 if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
916 if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
917 if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
918 if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
919 if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
920 if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
921 if isfield(structmd,'elementonbed'), md.mesh.elementonbed=structmd.elementonbed; end
922 if isfield(structmd,'elementonsurface'), md.mesh.elementonsurface=structmd.elementonsurface; end
923 if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
924 if isfield(structmd,'nodeonbed'), md.mesh.vertexonbed=structmd.nodeonbed; end
925 if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
926 if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
927 if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
928 if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]929 if isfield(structmd,'edges'),
930 md.mesh.edges=structmd.edges;
931 md.mesh.edges(isnan(md.mesh.edges))=-1;
932 end
[13692]933 if isfield(structmd,'y'), md.mesh.y=structmd.y; end
934 if isfield(structmd,'x'), md.mesh.x=structmd.x; end
935 if isfield(structmd,'z'), md.mesh.z=structmd.z; end
936 if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
[15771]937 if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]938 if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
939 if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]940
[13692]941 %Field changes
942 if (isfield(structmd,'type') & ischar(structmd.type)),
943 if strcmpi(structmd.type,'2d'), md.mesh.dimension=2; end
944 if strcmpi(structmd.type,'3d'), md.mesh.dimension=3; end
945 end
946 if isnumeric(md.verbose),
947 md.verbose=verbose;
948 end
[15768]949
[13692]950 if isfield(structmd,'spcvelocity'),
[15771]951 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
952 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
953 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
954 pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
955 pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
956 pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]957 end
958 if isfield(structmd,'spcvx'),
[15771]959 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
960 pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]961 end
962 if isfield(structmd,'spcvy'),
[15771]963 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
964 pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]965 end
966 if isfield(structmd,'spcvz'),
[15771]967 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
968 pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]969 end
[14620]970 if isfield(structmd,'pressureload'),
971 if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]972 pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
973 pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
974 pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]975 end
[13692]976 end
977 if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
978 pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
979 pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
980 pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
981 pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
982 pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
983 pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
984 pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
985 pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
986 end
987 if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
988 pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
989 pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
990 pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
991 pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
992 pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
993 pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
994 pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
995 pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
996 end
997 if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
998 if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
999 if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1000 if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1001 end
1002 if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1003 if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
1004 if (structmd.groundingline_migration==273), md.groundingline.migration='AgressiveMigration'; end
1005 if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1006 end
1007 if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1008 if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1009 if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1010 if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1011 end
1012 if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1013 pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1014 pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1015 pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1016 pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1017 pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1018 pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1019 pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1020 pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1021 pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1022 end
[11659]1023
[13692]1024 if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1025 md.thermal.stabilization=2;
[15767]1026 md.masstransport.stabilization=1;
[13692]1027 md.balancethickness.stabilization=1;
1028 end
[15767]1029 if isnumeric(md.masstransport.hydrostatic_adjustment)
1030 if md.masstransport.hydrostatic_adjustment==269,
1031 md.masstransport.hydrostatic_adjustment='Incremental';
[13692]1032 else
[15767]1033 md.masstransport.hydrostatic_adjustment='Absolute';
[13692]1034 end
1035 end
[8952]1036
[13692]1037 %New fields
1038 if ~isfield(structmd,'upperelements');
1039 md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1040 md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1041 end
1042 if ~isfield(structmd,'lowerelements');
1043 md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1044 md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1045 end
1046 if ~isfield(structmd,'diagnostic_ref');
[15771]1047 md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]1048 end
[14529]1049 if ~isfield(structmd,'loadingforce');
[15771]1050 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]1051 end
[15768]1052
1053 %2013 August 9
1054 if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1055 disp('Recovering old prognostic class');
1056 md.masstransport=masstransport(structmd.prognostic);
1057 end
[15771]1058 %2013 August 9
[15775]1059 if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') || isa(structmd.diagnostic,'stressbalance')),
[15771]1060 disp('Recovering old diagnostic class');
[15775]1061 md.stressbalance=stressbalance(structmd.diagnostic);
[15771]1062 end
[13692]1063 end% }}}
1064 function md = setdefaultparameters(md) % {{{
[8926]1065
[13692]1066 %initialize subclasses
1067 md.mesh = mesh();
1068 md.mask = mask();
1069 md.constants = constants();
1070 md.geometry = geometry();
1071 md.initialization = initialization();
[17079]1072 md.surfaceforcings = SMB();
[13692]1073 md.basalforcings = basalforcings();
1074 md.friction = friction();
1075 md.rifts = rifts();
1076 md.timestepping = timestepping();
1077 md.groundingline = groundingline();
1078 md.materials = matice();
[16160]1079 md.damage = damage();
[13692]1080 md.flowequation = flowequation();
1081 md.debug = debug();
[14558]1082 md.verbose = verbose();
[13692]1083 md.settings = settings();
[14621]1084 md.toolkits = toolkits();
[13692]1085 md.cluster = generic();
1086 md.balancethickness = balancethickness();
[17079]1087 md.stressbalance = stressbalance();
[14555]1088 md.hydrology = hydrologyshreve();
[17079]1089 md.masstransport = masstransport();
[13692]1090 md.thermal = thermal();
1091 md.steadystate = steadystate();
1092 md.transient = transient();
[14724]1093 md.gia = gia();
[13692]1094 md.autodiff = autodiff();
1095 md.flaim = flaim();
1096 md.inversion = inversion();
1097 md.qmu = qmu();
1098 md.radaroverlay = radaroverlay();
1099 md.results = struct();
[16388]1100 md.outputdefinition = outputdefinition();
[13692]1101 md.miscellaneous = miscellaneous();
1102 md.private = private();
1103 end
1104 %}}}
1105 function disp(obj) % {{{
1106 disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(obj.mesh) ']'],'mesh properties'));
1107 disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(obj.mask) ']'],'defines grounded and floating elements'));
1108 disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(obj.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1109 disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(obj.constants) ']'],'physical constants'));
1110 disp(sprintf('%19s: %-22s -- %s','surfaceforcings' ,['[1x1 ' class(obj.surfaceforcings) ']'],'surface forcings'));
1111 disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(obj.basalforcings) ']'],'bed forcings'));
1112 disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(obj.materials) ']'],'material properties'));
[17367]1113 disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(obj.damage) ']'],'parameters for damage evolution solution'));
[13692]1114 disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(obj.friction) ']'],'basal friction/drag properties'));
1115 disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(obj.flowequation) ']'],'flow equations'));
1116 disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(obj.timestepping) ']'],'time stepping for transient models'));
1117 disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(obj.initialization) ']'],'initial guess/state'));
1118 disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(obj.rifts) ']'],'rifts properties'));
1119 disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(obj.debug) ']'],'debugging tools (valgrind, gprof)'));
1120 disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
1121 disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
[14621]1122 disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(obj.toolkits) ']'],'PETSc options for each solution'));
[13692]1123 disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
1124 disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
[15771]1125 disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(obj.stressbalance) ']'],'parameters for stressbalance solution'));
[13692]1126 disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(obj.groundingline) ']'],'parameters for groundingline solution'));
1127 disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(obj.hydrology) ']'],'parameters for hydrology solution'));
[15767]1128 disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(obj.masstransport) ']'],'parameters for masstransport solution'));
[13692]1129 disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(obj.thermal) ']'],'parameters for thermal solution'));
1130 disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
1131 disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
[14724]1132 disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(obj.gia) ']'],'parameters for gia solution'));
[13692]1133 disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
1134 disp(sprintf('%19s: %-22s -- %s','flaim' ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
1135 disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(obj.inversion) ']'],'parameters for inverse methods'));
1136 disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(obj.qmu) ']'],'dakota properties'));
[16388]1137 disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(obj.outputdefinition) ']'],'output definition'));
[13692]1138 disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(obj.results) ']'],'model results'));
1139 disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(obj.radaroverlay) ']'],'radar image for plot overlay'));
1140 disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields'));
1141 end % }}}
[14307]1142 function memory(obj) % {{{
[15106]1143
[14611]1144 disp(sprintf('\nMemory imprint:\n'));
[14307]1145
[14603]1146 fields=properties('model');
1147 mem=0;
[15106]1148
[14603]1149 for i=1:length(fields),
1150 field=obj.(fields{i});
1151 s=whos('field');
1152 mem=mem+s.bytes/1e6;
[14611]1153 disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]1154 end
[14603]1155 disp(sprintf('%19s--%10s','--------------','--------------'));
1156 disp(sprintf('%19s: %g Mb','Total',mem));
[14307]1157 end % }}}
[14603]1158 function netcdf(obj,filename) % {{{
1159 %NETCDF - save model as netcdf
1160 %
1161 % Usage:
1162 % netcdf(md,filename)
1163 %
1164 % Example:
1165 % netcdf(md,'model.nc');
1166
1167 disp('Saving model as NetCDF');
1168 %1. Create NetCDF file
1169 ncid=netcdf.create(filename,'CLOBBER');
1170 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[14611]1171 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' obj.miscellaneous.name ')']);
[14603]1172 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1173 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1174
[14611]1175 %Preallocate variable id, needed to write variables in netcdf file
[14631]1176 var_id=zeros(1000,1);%preallocate
[14609]1177
1178 for step=1:2,
1179 counter=0;
[14612]1180 [var_id,counter]=structtonc(ncid,'md',obj,0,var_id,counter,step);
[14609]1181 if step==1, netcdf.endDef(ncid); end
[14603]1182 end
[14611]1183
[14631]1184 if counter>1000,
1185 warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]1186 end
1187
1188 netcdf.close(ncid)
[14603]1189 end % }}}
[14405]1190 function xylim(obj) % {{{
1191
1192 xlim([min(obj.mesh.x) max(obj.mesh.x)]);
1193 ylim([min(obj.mesh.y) max(obj.mesh.y)])
1194 end % }}}
[15316]1195 function md=upload(md) % {{{
1196 %the goal of this routine is to upload the model onto a server, and to empty it.
1197 %So first, save the model with a unique name and upload the file to the server:
1198 random_part=fix(rand(1)*10000);
1199 id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1200 eval(['save ' id ' md']);
1201
1202 %Now, upload the file:
1203 issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1204
1205 %Now, empty this model of everything except settings, and record name of file we just uploaded!
1206 settings_back=md.settings;
1207 md=model();
1208 md.settings=settings_back;
1209 md.settings.upload_filename=id;
1210
1211 %get locally rid of file that was uploaded
1212 eval(['delete ' id]);
1213
1214 end % }}}
1215 function md=download(md) % {{{
[15643]1216
[15316]1217 %the goal of this routine is to download the internals of the current model from a server, because
1218 %this model is empty, except for the settings which tell us where to go and find this model!
[15643]1219
[15316]1220 %Download the file:
1221 issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1222
1223 name=md.settings.upload_filename;
1224
1225 %Now, load this model:
1226 md=loadmodel(md.settings.upload_filename);
1227
1228 %get locally rid of file that was downloaded
1229 eval(['delete ' name]);
1230
1231 end % }}}
[13692]1232 end
[8926]1233 end
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