Index: /issm/trunk-jpl/src/m/mesh/bamg.py =================================================================== --- /issm/trunk-jpl/src/m/mesh/bamg.py (revision 27119) +++ /issm/trunk-jpl/src/m/mesh/bamg.py (revision 27120) @@ -23,92 +23,92 @@ Available options (for more details see ISSM website http://issm.jpl.nasa.gov/): - - domain : followed by an ARGUS file that + - domain : followed by an ARGUS file that prescribes the domain outline - - holes : followed by an ARGUS file that + - holes : followed by an ARGUS file that prescribes the holes - - subdomains : followed by an ARGUS file that - prescribes the list of subdomains + - subdomains : followed by an ARGUS file that + prescribes the list of subdomains (that need to be inside domain) - - hmin : minimum edge length (default is + - hmin : minimum edge length (default is 1.0e-100) - - hmax : maximum edge length (default is + - hmax : maximum edge length (default is 1.0e100) - - hVertices : imposed edge length for each vertex + - hVertices : imposed edge length for each vertex (geometry or mesh) - - hminVertices : minimum edge length for each vertex + - hminVertices : minimum edge length for each vertex (mesh) - - hmaxVertices : maximum edge length for each vertex + - hmaxVertices : maximum edge length for each vertex (mesh) - - anisomax : maximum ratio between the smallest - and largest edges (default is + - anisomax : maximum ratio between the smallest + and largest edges (default is 1.0e30) - - coeff : coefficient applied to the metric - (2 -> twice as many elements, + - coeff : coefficient applied to the metric + (2 -> twice as many elements, default is 1) - - cutoff : scalar used to compute the metric + - cutoff : scalar used to compute the metric when metric type 2 or 3 are applied - - err : error used to generate the metric + - 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 : 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 + - gradation : maximum ratio between two adjacent edges - - Hessiantype : 0 -> use double P2 projection + - Hessiantype : 0 -> use double P2 projection (default) 1 -> use Green formula - - KeepVertices : try to keep initial vertices when - adaptation is done on an existing + - KeepVertices : try to keep initial vertices when + adaptation is done on an existing mesh (default 1) - - NoBoundaryRefinement : do not refine boundary, only follow - contour provided (default 0). Allow - subdomain boundary refinement + - NoBoundaryRefinement : do not refine boundary, only follow + contour provided (default 0). Allow + subdomain boundary refinement though - - NoBoundaryRefinementAllBoundaries : do not refine boundary, only follow + - NoBoundaryRefinementAllBoundaries : do not refine boundary, only follow contour provided (default 0) - - maxnbv : maximum number of vertices used to + - maxnbv : maximum number of vertices used to allocate memory (default is 1.0e6) - - maxsubdiv : maximum subdivision of exisiting + - maxsubdiv : maximum subdivision of exisiting elements (default is 10) - - metric : matrix (numberofnodes x 3) used as + - metric : matrix (numberofnodes x 3) used as a metric - - Metrictype : 1 -> absolute error + - Metrictype : 1 -> absolute error c/(err coeff^2) * Abs(H) (default) - 2 -> relative error - c / (err coeff^2) * Abs(H) / + 2 -> relative error + c / (err coeff^2) * Abs(H) / max(s, cutoff * max(s)) - 3 -> rescaled absolute error - c / (err coeff^2) * Abs(H) / + 3 -> rescaled absolute error + c / (err coeff^2) * Abs(H) / (smax - smin) - - nbjacoby : correction used by Hessiantype = 1 + - nbjacoby : correction used by Hessiantype = 1 (default is 1) - - nbsmooth : number of metric smoothing + - nbsmooth : number of metric smoothing procedure (default is 3) - - omega : relaxation parameter of the - smoothing procedure (default is + - omega : relaxation parameter of the + smoothing procedure (default is 1.8) - - power : power applied to the metric + - power : power applied to the metric (default is 1) - - splitcorners : split triangles which have 3 - vertices on the outline (default is + - splitcorners : split triangles which have 3 + vertices on the outline (default is 1) - verbose : level of verbosity (default is 1) - - rifts : followed by an ARGUS file that + - rifts : followed by an ARGUS file that prescribes the rifts - - toltip : tolerance to move tip on an - existing point of the domain + - 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 + - tracks : followed by an ARGUS file that + prescribes the tracks that the mesh will stick to - - RequiredVertices : mesh vertices that are required. + - 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 : if the distance between 2 points of + the domain outline is less than tol, they will be merged @@ -250,9 +250,8 @@ # Flag how many edges we have now, that way we know which edges - # belong to the subdomain. Will be used later fo required edges + # belong to the subdomain. Will be used later fo required edges # if NoBoundaryRefinement equals 1. new_edge_length = len(bamg_geometry.Edges) - edges_required = range((edge_length + 1), (new_edge_length + 1)) # NOTE: Upper bound of range is non-inclusive (compare to src/m/mesh/bamg.m) - + edges_required = np.asarray(range((edge_length + 1), (new_edge_length + 1))) # NOTE: Upper bound of range is non-inclusive (compare to src/m/mesh/bamg.m) if i: # NOTE: same as `if i > 0` (MATLAB is `if i > 1`) bamg_geometry.SubDomains = np.vstack((bamg_geometry.SubDomains, [2, count + 1, 1, -subdomain_ref])) @@ -445,5 +444,5 @@ np.array([[count, count + 1, 2]]), np.hstack(( - np.arange(count + 1, count + nods).reshape(-1, ), + np.arange(count + 1, count + nods).reshape(-1, ), np.arange(count + 2, count + nods + 1).reshape(-1, ), (1 + i) * np.ones((nods - 1, 1)) @@ -455,5 +454,5 @@ nods = rift[i]['nods'] - 1 bamg_geometry.Vertices = np.vstack(( - bamg_geometry.Vertices, + bamg_geometry.Vertices, np.hstack(( rift[i]['x'][:],