FOSSIL

Appearance

FOSSILFOrtran Surfaces, Solids, Immersed boundaries and Level sets

The geometry of complex bodies for simulation codes, in pure Fortran: triangulated surfaces and 2-D curves read and repaired, signed distances and level sets, immersed-boundary queries, AMR tagging, exact cut cells and moving bodies, on the CPU or bit-exact on the GPU.

Tutorial
Cookbook
Reference
API
View on GitHub
the FOSSIL logo, an ammonite meshed in triangles and carved by lightthe FOSSIL logo, an ammonite meshed in triangles and carved by light
📂

STL in, STL out

ASCII or binary, format detected, NaN and Inf rejected with a status; analyze gives the box, volume, centroid, connectivity, shells and bodies.

I/O and analysis

🩹

Repair dirty meshes

sanitize removes slivers and duplicates, closes gaps and orients the normals outward; fill_holes patches and fairs the holes left.

Repair

📏

Signed distance

Closest facet on a SAH BVH, bit-exact against brute force; four sign algorithms, the fast winding number for surfaces with holes.

Distance and signs

🌊

Level sets

A signed-distance field on a stretched grid: exact narrow band, flood-fill signs, fast sweeping, an eikonal diagnostic.

Distance fields

〰️

2-D curves

Closed and open polylines for quadtree solvers, with the same queries as the surfaces; sections of any STL by a grid plane.

2-D geometry

🎯

Immersed-boundary queries

Per point: closest point, feature, pseudo-normal and body; image points and probes; wall distance with cutoff; wall curvature.

IB queries

🧭

AMR tagging

Blocks and cells classified as cut, near, inside or outside from the tree alone; signed tag bands on a block.

AMR tagging

🧱

Exact cut cells

Grid-line crossings decided by exact predicates; 2-D and 3-D fluid fractions, apertures and fluid pieces with their own volumes.

Cut cells

🔄

Moving bodies

Body-frame queries without a rebuild, an O(N) tree refit, and the swept geometry of a time step: exact swept volumes.

Moving bodies

🛠️

Geometry processing

Booleans, self-intersections, decimation, remeshing, smoothing, alpha wrapping, marching cubes, curvature, segmentation.

Surfaces

🚀

On the GPU, bit for bit

OpenACC kernels shared with the CPU path: distances, rich queries, tagging and posed queries equal the CPU results bit for bit.

GPU queries

🆓

Free and portable

Pure Fortran 2003+, no C; gfortran, ifx, nvfortran; FoBiS or fpm; GPLv3, BSD or MIT.

Installation

In a nutshell ​

Load a body, read what FOSSIL computed about it, save it (the first chapter of the tutorial):

f90
!< Tutorial 1: load an STL surface, read what analyze computed, save it.
program tut01_first_surface
use fossil, only : surface_stl_object
use penf,   only : I4P, R8P
use vecfor, only : vector_R8P

implicit none
type(surface_stl_object) :: surface
type(vector_R8P)         :: bmin, bmax

call surface%load_from_file(file_name='dragon.stl', guess_format=.true.) ! analyze runs inside
bmin = surface%get_bmin() ; bmax = surface%get_bmax()
print '(A,I0)',       'facets      ', surface%get_facets_number()
print '(A,3F10.4)',   'box min     ', bmin%x, bmin%y, bmin%z
print '(A,3F10.4)',   'box max     ', bmax%x, bmax%y, bmax%z
print '(A,F12.4)',    'volume      ', surface%get_volume()
print '(A,L1,A,L1)',  'watertight  ', surface%is_watertight(), '   manifold ', surface%is_manifold()
call surface%save_into_file(file_name='dragon-ascii.stl', is_ascii=.true.)
print '(A)', 'saved dragon-ascii.stl'
endprogram tut01_first_surface
$ tut01_first_surface
facets      6588
box min       -10.8287   -4.1883    5.2821
box max         9.6461    4.9512   19.7413
volume          465.9287
watertight  F   manifold F
saved dragon-ascii.stl

The dragon is neither watertight nor manifold as loaded: chapter 2 repairs it. Start with the tutorial, or look up a task in the cookbook.

See it run ​

animation: the exact cut cells of a NACA 0012 section pitching and translating through a 48 by 24 grid, each cell shaded by its solid fractionanimation: iso-distance contours from 0.05 to 0.6 around the same pitching section

A NACA 0012 section pitching and translating through a Cartesian grid, every frame computed by FOSSIL: its exact cut cells and the level sets of its signed distance, with the pose passed to the query instead of rebuilding the tree.

STL in, STL out: the dragon loaded, 6588 facets, and the box analyze computesSTL in, STL outthe dragon loaded, 6588 facets, and the box analyze computesRepair dirty meshes: holes closed one by one by fill_holes, refined and fairedRepair dirty meshesholes closed one by one by fill_holes, refined and fairedSigned distance: probes and their closest points on the dragonSigned distanceprobes and their closest points on the dragonLevel sets: the signed-distance field on a stretched gridLevel setsthe signed-distance field on a stretched grid2-D curves: a section of the dragon and its 2-D signed distance2-D curvesa section of the dragon and its 2-D signed distanceImmersed-boundary queries: closest points on a face, an edge or a vertexImmersed-boundary queriesclosest points on a face, an edge or a vertexAMR tagging: cut, inside and outside cells of a block, in signed bandsAMR taggingcut, inside and outside cells of a block, in signed bandsExact cut cells: the fluid fraction of the cut cells of a sectionExact cut cellsthe fluid fraction of the cut cells of a sectionMoving bodies: the area a moving section sweeps in a time stepMoving bodiesthe area a moving section sweeps in a time stepMass properties: a T-handle flipping about its intermediate axis, from its inertia tensorMass propertiesa T-handle flipping about its intermediate axis, from its inertia tensorSurface deviation: a decimation sweep coloured by its certified distance from the originalSurface deviationa decimation sweep coloured by its certified distance from the originalFeature edges: cells touching the sharp edges of a part, as the grid refinesFeature edgescells touching the sharp edges of a part, as the grid refinesThickness and gaps: a wing's walls thinner than the cell, shrinking to the trailing edgeThickness and gapsa wing's walls thinner than the cell, shrinking to the trailing edgeNamed patches: query points around a body, each coloured by the patch of its closest facetNamed patchesquery points around a body, each coloured by the patch of its closest facetBody-body distance: a cube closing on the dragon on a screw motion, its closest pair down to contactBody-body distancea cube closing on the dragon on a screw motion, its closest pair down to contactBooleans: a block drilled nine times, each step checked by an independent booleanBooleansa block drilled nine times, each step checked by an independent booleanOn the GPU, bit for bit: the device code path on a slice: 0 differences from the hostOn the GPU, bit for bitthe device code path on a slice: 0 differences from the hostFree and portable: the tutorial programs, run one after the otherFree and portablethe tutorial programs, run one after the other

Every figure and every program of the tutorial and of the cookbook is computed and run by scripts/docs_examples.sh: the outputs above are captured, not typed.

Authors ​

Copyrights ​

FOSSIL is distributed under a multi-licensing system: GPL v3 for FOSS projects, BSD 2-Clause, BSD 3-Clause or MIT for closed-source or commercial ones.