Feature map

Everything FOSSIL does, grouped as the reference is grouped. Each row names the entry point, the reference page and, where there is one, the tutorial chapter that uses it. Every public operation is a type-bound procedure of one of four types, surface_stl_object, curve_object, distance_field_object and facet_object, or a free procedure of a module of its own (named in the row); use fossil re-exports the types and the named constants.

Surfaces

Capability	Entry point	Reference	Tutorial	Cookbook
Load ASCII or binary STL, format detected, NaN/Inf rejected, optional clip box	surface%load_from_file	I/O, analysis, manipulation	1	1, 2, 3, 4
Save ASCII or binary STL	surface%save_into_file	I/O, analysis, manipulation	1	1
Bounding box, volume, centroid, connectivity, shells and bodies, pseudo-normals, AABB tree	surface%analyze (run by load, sanitize, clip)	I/O, analysis, manipulation	1	1
Validity: watertight, manifold, closed volume	is_watertight, is_manifold, is_volume	I/O, analysis, manipulation	2	1
Repair: slivers, duplicates, gaps, orientation, one warning per defect class	surface%sanitize	I/O, analysis, manipulation	2	1
Hole filling (Liepa minimum-weight patches, refinement, thin-plate fairing)	surface%fill_holes	Hole filling	2	1
Translate, rotate, mirror, resize, clip, merge	translate, rotate, mirror, resize, clip, merge_solids	I/O, analysis, manipulation	3	1, 2, 3
Self-intersection detection and resolution (exact pair_cut, exact predicates)	find_self_intersections, resolve_self_intersections	Self-intersection	12	1, 2
Booleans: union, intersection, difference, symmetric difference (Zhou et al. 2016)	surface%boolean	Boolean operations	12	1
Quadric decimation (Garland and Heckbert 1997)	surface%decimate	Mesh decimation		1, 2
Isotropic remeshing, optional feature preservation (Botsch and Kobbelt 2004)	surface%isotropic_remesh	Isotropic remeshing	12	1
Explicit and Taubin smoothing	surface%smooth	Mesh smoothing		1
Alpha wrapping: a watertight surrogate of any triangle soup (Portaneri et al. 2022)	surface%alpha_wrap	Alpha wrapping		1
Isosurface extraction (Lorensen and Cline 1987)	extract_isosurface	Marching cubes		1
Shape-diameter segmentation (Shapira et al. 2008)	surface%segment_sdf	SDF segmentation		1
Cotangent Laplacian and barycentric mass	surface%cotangent_laplacian	Cotangent Laplacian		1
Gaussian and mean curvature per vertex; pointwise O(h²) by a cubic jet fit	gaussian_curvature, mean_curvature, jet_curvature	Per-vertex curvature		1, 2
Mass, centre of mass, inertia tensor, principal axes (exact polyhedral integrals); 2-D second moments	surface%mass_properties, curve%mass_properties, inertia_to_world, principal_frame	Mass properties	12	1, 2, 3
Surface deviation: one-sided and symmetric Hausdorff distance, mean, rms, per-vertex distance	surface%deviation, surface%hausdorff, curve%deviation, curve%hausdorff	Surface deviation	12	1, 2
Feature edges: sharp, boundary and non-manifold edges, corners, polylines; refinement and distances along them; 2-D corners	surface%feature_edges, build_features, box_feature_many, tag_block(feature_tags=), query_many(feature_distances=), curve%feature_corners	Feature edges	12	1, 2, 3
Local thickness and gaps per facet: ray (shape diameter) and medial (shrinking ball); thin regions under a cell size; refinement of thin walls	surface%thickness, thin_regions, build_thin, box_thin_many, tag_block(thin_tags=), curve%thickness	Thickness and gaps	12	1, 2
Named patches: one per solid block or per file, kept on every facet; multi-solid ASCII output	load_from_files, get_patches_number, patch_name, facet_patch, set_patch	Named patches	12	1, 2
Distance between two bodies: closest facets and points, contact; bit-identical to brute force	surface%distance_to	Body–body distance	14	1
Time of first contact of moving bodies over a step: certified (never late, no tunnelling), several bodies, 2-D twins	surface%time_of_impact, curve%time_of_impact, first_impact, first_impact_2d	Continuous collision detection	14	1, 2

Distance and signs

Capability	Entry point	Reference	Tutorial	Cookbook
Signed or unsigned distance of a point, bit-exact against brute force	surface%distance	I/O, analysis, manipulation	4	1
Closest facet, edge, vertex, point and normal	surface%compute_distance	I/O, analysis, manipulation	4	1
Inside or outside	surface%is_point_inside	Sign algorithms benchmark	4	1
Four sign algorithms: pseudo-normal (default), ray parity, solid angle, fast winding number	sign_algorithm=	Sign algorithms benchmark	4	1
Generalized and fast winding number (Jacobson 2013, Barill 2018)	surface%winding_number	Winding number		1
Batched distances, OpenMP-parallel and bit-exact with serial	surface%distance_many	I/O, analysis, manipulation	5	1
SAH BVH (default) or octree acceleration	aabb_tree_kind=	I/O, analysis, manipulation	5	1
Read-only access to the acceleration tree: node boxes down to a depth, leaves and their facets (both kinds; curve twin)	surface%tree_boxes, curve%tree_boxes	I/O, analysis, manipulation	5	1
Ray queries: first hit, all hits (one per crossing, exact), any hit	intersect_ray_first, _all, _any	Ray queries		1
Signed-distance field on a stretched grid: exact band, flood-fill signs, fast sweeping	distance_field_object%compute	Signed-distance fields	6	1
Eikonal diagnostic of a field	distance_field_object%gradient_diagnostic	Signed-distance fields		1

Immersed boundaries

Capability	Entry point	Reference	Tutorial	Cookbook
2-D curves: closed and open polylines, segment BVH, signed distance, 2-D winding number, repair	curve_object	2-D geometry	7	1
Axis-aligned section of an STL as a curve	slice_surface	2-D geometry	7	1
Rich queries: closest point, feature, pseudo-normal, body; ambiguous feet; wall curvature	query_point, query_many	Immersed-boundary queries	8	1, 2
Image points and probes with a visibility test	image_points, probe_many	Immersed-boundary queries	8	1
Wall distance with body id and early cutoff	wall_distance_many	Immersed-boundary queries		1
Grid-adapted markers	surface_markers, curve_markers	Immersed-boundary queries		1, 2
AMR block and cell classification: cut, near, inside, outside	box_classify_many	AMR tagging	9	1
Signed tag bands on a block	tag_block	AMR tagging	9	1
Exact grid-line crossings and wall fractions	line_crossings, cell_wall_fractions	Cut-cell geometry		1, 2
2-D cut cells: fractions, apertures, centroids, wetted boundary, pieces	curve%cut_cells	Cut-cell geometry	10	1, 2
3-D cut cells: face fractions, volumes, fluid pieces with their own measures	cut_cells_3d (module fossil_cut_cells_3d)	Cut-cell geometry	10	1
Cut-cell solver support: piece links, state- and flux-redistribution neighbourhoods, merge targets	cut_links_2d, cut_cells_3d(links=), srd_neighbourhoods, frd_neighbourhoods, merge_targets	Cut cells: solver support		1, 2
Cut-cell moments up to order 4, quadrature rules, edge fractions, exact coarsening	cut_cells_3d(moments_order=, quadrature=, edges=), curve%cut_cells(moments_order=, quadrature=), cut_coarsen_3d, cut_coarsen_2d	Cut cells: solver support		1, 2, 3
Curvilinear structured blocks: topology records (seams, cuts, poles, periodic, interfaces) and their detection	curvilinear_block_t, curvilinear_block_2d_t, detect_topology	Curvilinear blocks	13	1, 2
Exact cell geometry, certified cell validity, quality metrics	geometry, validity, quality	Curvilinear blocks	13	1
Point location in curvilinear blocks (robust, walking, GPU) and Lagrange stencils of width q	locate_many, locate_many_device, locate_in_blocks, stencils	Curvilinear blocks	13	1, 2, 3
Overset cutters and hole cutting: wall cutters with trimming, exact hole flags (CPU and GPU), hole maps, X-rays	wall_cutter, hole_flags, hole_map, xray_flags	Overset assembly	13	1, 2
Overset donors and classification: candidates with quality (CPU and GPU), pair matrix, explicit and implicit selection, fringes, orphans by cause, overlap width, wall projection, moving grids, connectivity output	donor_candidates, classify, fringe_levels, wall_projection, exposed_points, build_connectivity	Overset assembly	13	1, 2, 3, 4, 5
Body-fitted grid support: constrained projection onto bodies (patches, feature and patch-boundary curves, corners), block faces, wall-spacing and quality report (y1, y1+, growth), 2-D hyperbolic extrusion	projection_target, project_points, project_block_face, block_report, hyperbolic_grid_2d	Body-fitted grid support	15	1, 2, 3, 4, 5
Rigid poses, body-frame queries, O(N) tree refit	rigid_pose_t, pose=, move	Moving bodies	11	1
Swept geometry of a time step: exact swept volumes, time-averaged apertures	swept_cells_2d, swept_cells_3d	Moving bodies	11	1, 2

GPU

Capability	Entry point	Reference	Tutorial	Cookbook
Distance, rich queries, wall distance, box classification, posed queries on the device (OpenACC), bit-exact against the CPU path	enter_device, *_device, exit_device	GPU queries	16	1, 2

fossilizer CLI

src/app/fossilizer.f90 wraps the library for the command line: load one or more STL files, clip, merge, mirror, rotate, translate, resize, sanitize and repair connectivity, print statistics and, with --mass_properties [--density ρ], the mass properties of a closed body, or with --compare other.stl, the certified Hausdorff distance to another surface, or with --distance other.stl, the body–body distance, or with --patches prefix, the named patches (one STL per patch), or with --features file.vtk, the feature edges and corners, or with --thickness file.vtk [--thickness_method ray|medial] [--h h --thin_factor f], the thinnest wall, the narrowest gap and the facets thinner than the cell; save the result.

Compilers

Compiler	Status
GNU gfortran 14.3+ (14 series) or ≥ 15.1	Supported (13.x and 14.0–14.2 untested, see Installation)
Intel Fortran ≥ 16.x	Supported
NVIDIA HPC Fortran (nvfortran) ≥ 26.9	The device build of the GPU queries, compiled without FMA contraction

Design principles

• Pure Fortran: no C extensions, no system calls beyond standard I/O.
• Exact where it decides: orientation predicates are exact (orient2d, orient3d); tree-accelerated queries equal brute force bit for bit; the GPU path equals the CPU path bit for bit.
• OOP and TDD: every operation is a type-bound procedure, every public operation is exercised by a test in src/tests/.
• Free and open source: multi-licensed for FOSS and commercial use.