Index: /issm/branches/trunk-larour-NatGeoScience2016/src/m/mesh/bamg.m =================================================================== --- /issm/branches/trunk-larour-NatGeoScience2016/src/m/mesh/bamg.m (revision 22095) +++ /issm/branches/trunk-larour-NatGeoScience2016/src/m/mesh/bamg.m (revision 22095) @@ -0,0 +1,555 @@ +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) +% - NoBoundaryRefinment: do not refine boundary, only follow contour provided (default 0) +% - 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 : 0 -> absolute error c/(err coeff^2) * Abs(H) (default) +% 1 -> relative error c/(err coeff^2) * Abs(H)/max(s,cutoff*max(s)) +% 2 -> 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) +% - 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 + + %Deal with RequiredEdges + if getfieldvalue(options,'NoBoundaryRefinment',0)==1, + bamg_geometry.RequiredEdges=[1:size(bamg_geometry.Edges,1)]'; + 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.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.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 % }}}