Index: sm/branches/trunk-larour-NatGeoScience2016/src/m/mesh/bamg.m =================================================================== --- /issm/branches/trunk-larour-NatGeoScience2016/src/m/mesh/bamg.m (revision 22086) +++ (revision ) @@ -1,554 +1,0 @@ -function md=bamg(md,varargin) -%BAMG - mesh generation -% -% Available options (for more details see ISSM website http://issm.jpl.nasa.gov/): -% -% - domain : followed by an ARGUS file that prescribes the domain outline -% - hmin : minimum edge length (default is 10^-100) -% - hmax : maximum edge length (default is 10^100) -% - hVertices : imposed edge length for each vertex (geometry or mesh) -% - hminVertices : minimum edge length for each vertex (mesh) -% - hmaxVertices : maximum edge length for each vertex (mesh) -% -% - anisomax : maximum ratio between the smallest and largest edges (default is 10^30) -% - coeff : coefficient applied to the metric (2-> twice as many elements, default is 1) -% - cutoff : scalar used to compute the metric when metric type 2 or 3 are applied -% - err : error used to generate the metric from a field -% - errg : geometric error (default is 0.1) -% - field : field of the model that will be used to compute the metric -% to apply several fields, use one column per field -% - gradation : maximum ratio between two adjacent edges -% - Hessiantype : 0 -> use double L2 projection (default) -% 1 -> use Green formula -% - KeepVertices : try to keep initial vertices when adaptation is done on an existing mesh (default 1) -% - MaxCornerAngle : maximum angle of corners in degree (default is 10) -% - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) -% - maxsubdiv : maximum subdivision of exisiting elements (default is 10) -% - metric : matrix (numberofnodes x 3) used as a metric -% - Metrictype : 1 -> absolute error c/(err coeff^2) * Abs(H) (default) -% 2 -> relative error c/(err coeff^2) * Abs(H)/max(s,cutoff*max(s)) -% 3 -> rescaled absolute error c/(err coeff^2) * Abs(H)/(smax-smin) -% - nbjacoby : correction used by Hessiantype=1 (default is 1) -% - nbsmooth : number of metric smoothing procedure (default is 3) -% - omega : relaxation parameter of the smoothing procedure (default is 1.8) -% - power : power applied to the metric (default is 1) -% - splitcorners : split triangles whuch have 3 vertices on the outline (default is 1) -% - geometricalmetric : take the geometry into account to generate the metric (default is 0) -% - verbose : level of verbosity (default is 1) -% -% - vertical : is this a 2d vertical mesh (flowband, default is 0) -% - rifts : followed by an ARGUS file that prescribes the rifts -% - toltip : tolerance to move tip on an existing point of the domain outline -% - tracks : followed by an ARGUS file that prescribes the tracks that the mesh will stick to -% - RequiredVertices : mesh vertices that are required. [x,y,ref]; ref is optional -% - tol : if the distance between 2 points of the domain outline is less than tol, they -% will be merged -% -% Examples: -% md=bamg(md,'domain','DomainOutline.exp','hmax',3000); -% md=bamg(md,'field',[md.inversion.vel_obs md.geometry.thickness],'hmax',20000,'hmin',1000); -% md=bamg(md,'metric',A,'hmin',1000,'hmax',20000,'gradation',3,'anisomax',1); - -%process options -options=pairoptions(varargin{:}); -options=deleteduplicates(options,1); - -%initialize the structures required as input of Bamg -bamg_options=struct(); -bamg_geometry=bamggeom(); -bamg_mesh=bamgmesh(); - -% Bamg Geometry parameters {{{ -if exist(options,'domain'), - - %Check that file exists - domainfile=getfieldvalue(options,'domain'); - if ischar(domainfile), - if ~exist(domainfile,'file') error(['bamg error message: file ' domainfile ' not found']); end - - %read domain according to its extension: - [path,name,ext]=fileparts(domainfile); - if strcmp(ext,'.exp'), - domain=expread(domainfile); - elseif strcmp(ext,'.shp'), - domain=shpread(domainfile); - else - error(['bamg error message: file ' domainfile ' format not supported (.shp or .exp)']); - end - elseif isstruct(domainfile), - domain = domainfile; - else - error('''domain'' type not supported yet'); - end - - %Build geometry - count=0; - for i=1:length(domain), - - %Check that the domain is closed - if (domain(i).x(1)~=domain(i).x(end) | domain(i).y(1)~=domain(i).y(end)), - error('bamg error message: all contours provided in ''domain'' should be closed'); - end - - %Checks that all holes are INSIDE the principle domain outline - if i>1, - flags=ContourToNodes(domain(i).x,domain(i).y,domain(1),0); - if any(~flags), - error('bamg error message: All holes should be strictly inside the principal domain'); - end - end - - %Add all points to bamg_geometry - nods=domain(i).nods-1; %the domain are closed 1=end; - bamg_geometry.Vertices=[bamg_geometry.Vertices; [domain(i).x(1:nods) domain(i).y(1:nods) ones(nods,1)]]; - bamg_geometry.Edges =[bamg_geometry.Edges; [transpose(count+1:count+nods) transpose([count+2:count+nods count+1]) 1.*ones(nods,1)]]; - if i>1, bamg_geometry.SubDomains=[bamg_geometry.SubDomains; 2 count+1 1 1]; end - - %update counter - count=count+nods; - end - if getfieldvalue(options,'vertical',0), - if numel(getfieldvalue(options,'Markers',[]))~=size(bamg_geometry.Edges,1), - error(['for 2d vertical mesh, ''Markers'' option is required, and should be of size ' num2str(size(bamg_geometry.Edges,1))]); - end - end - if numel(getfieldvalue(options,'Markers',[]))==size(bamg_geometry.Edges,1), - bamg_geometry.Edges(:,3)=getfieldvalue(options,'Markers'); - end - - %take care of rifts - if exist(options,'rifts'), - - %Check that file exists - riftfile=getfieldvalue(options,'rifts'); - [pathr,namer,extr]=fileparts(riftfile); - if ~exist(riftfile,'file') - error(['bamg error message: file ' riftfile ' not found ']); - elseif strcmp(extr,'.exp'), - rift=expread(riftfile); - elseif strcmp(extr,'.shp'), - rift=shpread(riftfile); - end - %read rift file according to its extension: - [path,name,ext]=fileparts(riftfile); - if strcmp(ext,'.exp'), - rift=expread(riftfile); - elseif strcmp(ext,'.shp'), - rift=shpread(riftfile); - else - error(['bamg error message: file ' riftfile ' format not supported (.shp or .exp)']); - end - - for i=1:length(rift), - - %detect whether all points of the rift are inside the domain - flags=ContourToNodes(rift(i).x,rift(i).y,domain(1),0); - if ~flags, - error('one rift has all its points outside of the domain outline'), - - elseif any(~flags), - %We LOTS of work to do - disp('Rift tip outside of or on the domain has been detected and is being processed...'); - - %check that only one point is outside (for now) - if sum(~flags)~=1, - error('bamg error message: only one point outside of the domain is supported yet'); - end - - %Move tip outside to the first position - if flags(1)==0, - %OK, first point is outside (do nothing), - elseif (flags(end)==0), - rift(i).x=flipud(rift(i).x); - rift(i).y=flipud(rift(i).y); - else - error('bamg error message: only a rift tip can be outside of the domain'); - end - - %Get cordinate of intersection point - x1=rift(i).x(1); y1=rift(i).y(1); - x2=rift(i).x(2); y2=rift(i).y(2); - for j=1:length(domain(1).x)-1; - if SegIntersect([x1 y1; x2 y2],[domain(1).x(j) domain(1).y(j); domain(1).x(j+1) domain(1).y(j+1)]), - - %Get position of the two nodes of the edge in domain - i1=j; - i2=j+1; - - %rift is crossing edge [i1 i2] of the domain - %Get coordinate of intersection point (http://mathworld.wolfram.com/Line-LineIntersection.html) - x3=domain(1).x(i1); y3=domain(1).y(i1); - x4=domain(1).x(i2); y4=domain(1).y(i2); - x=det([det([x1 y1; x2 y2]) x1-x2;det([x3 y3; x4 y4]) x3-x4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); - y=det([det([x1 y1; x2 y2]) y1-y2;det([x3 y3; x4 y4]) y3-y4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); - - segdis= sqrt((x4-x3)^2+(y4-y3)^2); - tipdis=[sqrt((x-x3)^2+(y-y3)^2) sqrt((x-x4)^2+(y-y4)^2)]; - - if (min(tipdis)/segdis) < getfieldvalue(options,'toltip',0), - disp('moving tip-domain intersection point'); - - %Get position of the closer point - if tipdis(1)>tipdis(2), - pos=i2; - else - pos=i1; - end - - %This point is only in Vertices (number pos). - %OK, now we can add our own rift - nods=rift(i).nods-1; - bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(2:end) rift(i).y(2:end) ones(nods,1)]]; - bamg_geometry.Edges=[bamg_geometry.Edges;... - pos count+1 (1+i);... - [transpose(count+1:count+nods-1) transpose(count+2:count+nods) (1+i)*ones(nods-1,1)]]; - count=count+nods; - - break; - - else - %Add intersection point to Vertices - bamg_geometry.Vertices=[bamg_geometry.Vertices; x y 1]; - count=count+1; - - %Decompose the crossing edge into 2 subedges - pos=find(bamg_geometry.Edges(:,1)==i1 & bamg_geometry.Edges(:,2)==i2); - if isempty(pos) error('bamg error message: a problem occurred...'); end - bamg_geometry.Edges=[bamg_geometry.Edges(1:pos-1,:);... - bamg_geometry.Edges(pos,1) count bamg_geometry.Edges(pos,3);... - count bamg_geometry.Edges(pos,2) bamg_geometry.Edges(pos,3);... - bamg_geometry.Edges(pos+1:end,:)]; - - %OK, now we can add our own rift - nods=rift(i).nods-1; - bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(2:end) rift(i).y(2:end) ones(nods,1)]]; - bamg_geometry.Edges=[bamg_geometry.Edges;... - count count+1 2 ;... - [transpose(count+1:count+nods-1) transpose(count+2:count+nods) (1+i)*ones(nods-1,1)]]; - count=count+nods; - - break; - end - end - end - else - nods=rift(i).nods-1; - bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(:) rift(i).y(:) ones(nods+1,1)]]; - bamg_geometry.Edges=[bamg_geometry.Edges; [transpose(count+1:count+nods) transpose(count+2:count+nods+1) (1+i)*ones(nods,1)]]; - count=count+nods+1; - end - end - end - - %Deal with tracks - if exist(options,'tracks'), - - %read tracks - track=getfieldvalue(options,'tracks'); - if all(ischar(track)), - A=expread(track); - track=[]; - for i=1:length(A), - track=[track; [A(i).x A(i).y]]; - end - else - track=double(track); %for some reason, it is of class "single" - end - if(size(track,2)==2), track=[track 3.*ones(size(track,1),1)]; end - - %only keep those inside - flags=ContourToNodes(track(:,1),track(:,2),domainfile,0); - track=track(find(flags),:); - - %Add all points to bamg_geometry - nods=size(track,1); - bamg_geometry.Vertices=[bamg_geometry.Vertices; track]; - bamg_geometry.Edges=[bamg_geometry.Edges; [transpose(count+1:count+nods-1) transpose(count+2:count+nods) 3.*ones(nods-1,1)]]; - - %update counter - count=count+nods; - end - - %Deal with vertices that need to be kept by mesher - if exist(options,'RequiredVertices'), - - %recover RequiredVertices - requiredvertices=double(getfieldvalue(options,'RequiredVertices')); %for some reason, it is of class "single" - if(size(requiredvertices,2)==2), requiredvertices=[requiredvertices 4.*ones(size(requiredvertices,1),1)]; end - - %only keep those inside - flags=ContourToNodes(requiredvertices(:,1),requiredvertices(:,2),domain(1),0); - requiredvertices=requiredvertices(find(flags),:); - - %Add all points to bamg_geometry - nods=size(requiredvertices,1); - bamg_geometry.Vertices=[bamg_geometry.Vertices; requiredvertices]; - - %update counter - count=count+nods; - - end - - %process geom - %bamg_geometry=processgeometry(bamg_geometry,getfieldvalue(options,'tol',NaN),domain(1)); - -elseif isstruct(md.private.bamg) & isfield(md.private.bamg,'geometry'), - bamg_geometry=bamggeom(md.private.bamg.geometry); -else - %do nothing... -end -%}}} -% Bamg Mesh parameters {{{ -if (~exist(options,'domain') & md.mesh.numberofvertices~=0 & strcmp(elementtype(md.mesh),'Tria')), - - if isstruct(md.private.bamg) & isfield(md.private.bamg,'mesh'), - bamg_mesh=bamgmesh(md.private.bamg.mesh); - else - bamg_mesh.Vertices=[md.mesh.x md.mesh.y ones(md.mesh.numberofvertices,1)]; - bamg_mesh.Triangles=[md.mesh.elements ones(md.mesh.numberofelements,1)]; - end - - if isstruct(md.rifts.riftstruct) - error('bamg error message: rifts not supported yet. Do meshprocessrift AFTER bamg'); - end -end -%}}} -% Bamg Options {{{ -bamg_options.Crack=getfieldvalue(options,'Crack',0); -bamg_options.anisomax=getfieldvalue(options,'anisomax',10.^30); -bamg_options.coeff=getfieldvalue(options,'coeff',1.); -bamg_options.cutoff=getfieldvalue(options,'cutoff',10.^-5); -bamg_options.err=getfieldvalue(options,'err',0.01); -bamg_options.errg=getfieldvalue(options,'errg',0.1); -bamg_options.field=getfieldvalue(options,'field',[]); -bamg_options.gradation=getfieldvalue(options,'gradation',1.5); -bamg_options.Hessiantype=getfieldvalue(options,'Hessiantype',0); -bamg_options.hmin=getfieldvalue(options,'hmin',10.^-100); -bamg_options.hmax=getfieldvalue(options,'hmax',10.^100); -bamg_options.hminVertices=getfieldvalue(options,'hminVertices',[]); -bamg_options.hmaxVertices=getfieldvalue(options,'hmaxVertices',[]); -bamg_options.hVertices=getfieldvalue(options,'hVertices',[]); -bamg_options.KeepVertices=getfieldvalue(options,'KeepVertices',1); -bamg_options.MaxCornerAngle=getfieldvalue(options,'MaxCornerAngle',10.); -bamg_options.maxnbv=getfieldvalue(options,'maxnbv',10^6); -bamg_options.maxsubdiv=getfieldvalue(options,'maxsubdiv',10.); -bamg_options.metric=getfieldvalue(options,'metric',[]); -bamg_options.Metrictype=getfieldvalue(options,'Metrictype',0); -bamg_options.nbjacobi=getfieldvalue(options,'nbjacobi',1); -bamg_options.nbsmooth=getfieldvalue(options,'nbsmooth',3); -bamg_options.omega=getfieldvalue(options,'omega',1.8); -bamg_options.power=getfieldvalue(options,'power',1.); -bamg_options.splitcorners=getfieldvalue(options,'splitcorners',1); -bamg_options.geometricalmetric=getfieldvalue(options,'geometricalmetric',0); -bamg_options.random=getfieldvalue(options,'rand',true); -bamg_options.verbose=getfieldvalue(options,'verbose',1); -%}}} - -%call Bamg -[bamgmesh_out bamggeom_out]=BamgMesher(bamg_mesh,bamg_geometry,bamg_options); - -if getfieldvalue(options,'vertical',0), - md.mesh=mesh2dvertical(); - md.mesh.x=bamgmesh_out.Vertices(:,1); - md.mesh.y=bamgmesh_out.Vertices(:,2); - md.mesh.elements=bamgmesh_out.Triangles(:,1:3); - md.mesh.edges=bamgmesh_out.IssmEdges; - md.mesh.segments=bamgmesh_out.IssmSegments(:,1:3); - md.mesh.segmentmarkers=bamgmesh_out.IssmSegments(:,4); - - %Fill in rest of fields: - md.mesh.numberofelements=size(md.mesh.elements,1); - md.mesh.numberofvertices=length(md.mesh.x); - md.mesh.numberofedges=size(md.mesh.edges,1); - md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; - - %Now, build the connectivity tables for this mesh. - md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; - -elseif getfieldvalue(options,'3dsurface',0), - - md.mesh=mesh3dsurface(); - md.mesh.x=bamgmesh_out.Vertices(:,1); - md.mesh.y=bamgmesh_out.Vertices(:,2); - md.mesh.z=md.mesh.x; md.mesh.z(:)=0; - md.mesh.elements=bamgmesh_out.Triangles(:,1:3); - md.mesh.edges=bamgmesh_out.IssmEdges; - md.mesh.segments=bamgmesh_out.IssmSegments(:,1:3); - md.mesh.segmentmarkers=bamgmesh_out.IssmSegments(:,4); - - %Fill in rest of fields: - md.mesh.numberofelements=size(md.mesh.elements,1); - md.mesh.numberofvertices=length(md.mesh.x); - md.mesh.numberofedges=size(md.mesh.edges,1); - md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; - -else - md.mesh=mesh2d(); - md.mesh.x=bamgmesh_out.Vertices(:,1); - md.mesh.y=bamgmesh_out.Vertices(:,2); - md.mesh.elements=bamgmesh_out.Triangles(:,1:3); - md.mesh.edges=bamgmesh_out.IssmEdges; - md.mesh.segments=bamgmesh_out.IssmSegments(:,1:3); - md.mesh.segmentmarkers=bamgmesh_out.IssmSegments(:,4); - - %Fill in rest of fields: - md.mesh.numberofelements=size(md.mesh.elements,1); - md.mesh.numberofvertices=length(md.mesh.x); - md.mesh.numberofedges=size(md.mesh.edges,1); - md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1; -end - -%Bamg private fields -md.private.bamg=struct(); -md.private.bamg.mesh=bamgmesh(bamgmesh_out); -md.private.bamg.geometry=bamggeom(bamggeom_out); -md.mesh.elementconnectivity=md.private.bamg.mesh.ElementConnectivity; -md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0; - -%Check for orphan -if any(~ismember(1:md.mesh.numberofvertices,sort(unique(reshape(md.mesh.elements,3*md.mesh.numberofelements,1))))) - error('Output mesh has orphans. Decrease MaxCornerAngle to prevent outside points (ex: 0.01)'); -end -end - -function geom=processgeometry(geom,tol,outline) % {{{ - -%Deal with edges -disp('Checking Edge crossing...'); -i=0; -while (ii); - geom.Edges(posedges)=geom.Edges(posedges)-1; - - %update counter - i=i-1; - end -end -if num, - disp(['WARNING: ' num2str(num) ' points outside the domain outline have been removed']); -end - -%Check point spacing -if ~isnan(tol), - disp('Checking point spacing...'); - i=0; - while (ij); - geom.Edges(posedges)=geom.Edges(posedges)-1; - - %update counter - j=j-1; - - end - end - end -end -%remove empty edges -geom.Edges(find(geom.Edges(:,1)==geom.Edges(:,2)),:)=[]; -end % }}} Index: /issm/branches/trunk-larour-NatGeoScience2016/src/m/mesh/patchglobe.m =================================================================== --- /issm/branches/trunk-larour-NatGeoScience2016/src/m/mesh/patchglobe.m (revision 22086) +++ /issm/branches/trunk-larour-NatGeoScience2016/src/m/mesh/patchglobe.m (revision 22087) @@ -73,5 +73,5 @@ %mesh: - mdb=bamg(model(),'domain',[temproot '/PatchBand.exp'],'MaxCornerAngle',1e-15,'gradation',10000); + mdb=bamg(model(),'domain',[temproot '/PatchBand.exp'],'MaxCornerAngle',1e-15,'gradation',10000,'NoBoundaryRefinment',1); mhb=mdb.mesh; clear mdb;