Issue with collisions, possibly related to CGAL plugin and/or Tetra2TriangleTopologicalMapping #4346

aleblanc30 · 2023-12-11T09:23:58Z

aleblanc30
Dec 11, 2023

I am building a simple simulation of a soft body and am stumped by an issue with collisions.

I am a fine visual mesh, which I use in conjunction with the CGAL plugin to create a coarse tetrahedral simulation mesh. The FEM simulation on this mesh seems to work fine.

Visual mesh :

Simulation mesh:

I then decided to implement collisions with a floor from STLIB. I wanted to use the coarse mesh for collision handling, so I used a topological mapping to populate a TriangleTopologyContainer with the border of the tetrahedral mesh. When I run the simulation, the collision mesh looks fine at first, but collisions are not detected on the outside. However, the topological mapping seems to leave behind isolated vertices inside the mesh.
Collision mesh :

Isolated points inside :

It appears that the collision pipeline only considers these isolated vertices, which makes for a rather unsightly result...

From the side :

From the top :

To code the collision, I took inspiration from various examples and these topics : https://www.sofa-framework.org/community/forum/topic/how-to-extract-the-surface-of-a-volumeyric-mesh/ ; #4033

Obviously the most likely explanation is that I am doing something wrong. I do however get a bunch of warnings probably related :

[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 135 109 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 109 9 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 9 135 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 144 73 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 73 10 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 10 144 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 73 137 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 137 10 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 300 269 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 269 78 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 78 300 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 197 160 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 160 77 for: 0 points.
[WARNING] [TriangleSetTopologyContainer(Container)] EdgesAroundVertex creation failed, Edge buffer is not concistent with number of points: Edge: 77 197 for: 0 points.

Any help would be appreciated !

Here is my code for this simulation :

import Sofa
from stlib3.scene import ContactHeader
from stlib3.physics.rigid import Floor

# Units : mm and kg

def createScene(rootNode):
    
    rootNode.findData('dt').value = 0.01
    rootNode.findData('gravity').value = [0, 0, -9180] # gravity is disabled
    rootNode.addObject('VisualStyle',
                       displayFlags='showCollision showVisualModels showForceFields showInteractionForceFields'
                                     +' hideCollisionModels hideBoundingCollisionModels hideWireframe')
    
    rootNode.bbox = "-50 -50 -50 50 50 50" # field of view of the viewer

    # Required plugins
    rootNode.addObject('RequiredPlugin', pluginName=[
                            "Sofa.Component.AnimationLoop",  # Needed to use components FreeMotionAnimationLoop
                            "Sofa.Component.Constraint.Lagrangian.Correction", # Needed to use components LinearSolverConstraintCorrection
                            "Sofa.Component.Constraint.Lagrangian.Solver",  # Needed to use components GenericConstraintSolver
                            "Sofa.Component.Constraint.Projective",  # Needed to use components FixedConstraint
                            "Sofa.Component.Engine.Select",  # Needed to use components BoxROI
                            "Sofa.Component.IO.Mesh",  # Needed to use components MeshVTKLoader
                            "Sofa.Component.LinearSolver.Direct",  # Needed to use components SparseLDLSolver
                            "Sofa.Component.LinearSolver.Iterative",  # Needed to use components ShewchukPCGLinearSolver
                            "Sofa.Component.Mass",  # Needed to use components UniformMass
                            "Sofa.Component.ODESolver.Backward",  # Needed to use components EulerImplicitSolver
                            "Sofa.Component.SolidMechanics.FEM.Elastic",  # Needed to use components TetrahedronFEMForceField
                            "Sofa.Component.Topology.Container.Constant",  # Needed to use components MeshTopology
                            "Sofa.Component.Visual",  # Needed to use components VisualStyle
                            "Sofa.Component.Mapping.Linear", # Needed to use components BarycentricMapping  
                            "Sofa.Component.StateContainer", # Needed to use components MechanicalObject
                            "Sofa.Component.Setting", # Needed to use components BackgroundSetting  
                            "Sofa.Component.Topology.Container.Dynamic", # Needed to use components TetrahedronSetGeometryAlgorithms,TetrahedronSetTopologyContainer  
                            "Sofa.GL.Component.Rendering3D", # Needed to use components OglModel,OglSceneFrame
                            "CGALPlugin", # Needed to use MeshGenerationFromPolyhedron
                            "SoftRobots",
                            "SofaPython3"
                        ])
    
    rootNode.addObject('BackgroundSetting', color=[0, 0.168627, 0.211765, 1]) # set background color
    rootNode.addObject('OglSceneFrame', style="Arrows", alignment="TopRight") # add a triedron to help with orientation

    # setup the animation loop
    rootNode.addObject('FreeMotionAnimationLoop')
    rootNode.addObject('GenericConstraintSolver', maxIterations=500, tolerance=1e-8)

    # add a collision pipeline
    ContactHeader(rootNode, alarmDistance=1, contactDistance=.01)

    # Add a floor
    Floor(rootNode, rotation=[90, 0, 0], translation=[0,0,-10], isAStaticObject=True)

    # create the larva object
    larvaBody = rootNode.addChild('larvaBody')

    # load the detailed mesh
    larvaSTL = '/home/alexandre/workspace/larva_meshing/mesh_cuticle_simplified.stl'
    larvaBody.addObject('MeshSTLLoader', name='larvaMesh', filename=larvaSTL)
    
    # create the overall body mechanics
    bodyMechanics = larvaBody.addChild('bodyMechanics')
    
    # use CGAL to create a simplified tetrahedral mesh of the larva
    bodyMechanics.addObject('MeshGenerationFromPolyhedron', name='gen', template='Vec3d', inputPoints='@../larvaMesh.position', inputTriangles='@../larvaMesh.triangles', drawTetras='0',
                       cellSize="10", facetAngle="30", facetSize="5", cellRatio="2",   #Convergence problem if lower than 2
                       facetApproximation="1")
    
    # Create the state from the coarse mesh
    bodyMechanics.addObject('MechanicalObject', name="dofs", position="@gen.outputPoints")
    bodyMechanics.addObject('TetrahedronSetTopologyContainer', name='topo', tetrahedra='@gen.outputTetras')
    bodyMechanics.addObject('TetrahedronSetGeometryAlgorithms', template="Vec3d", name="GeomAlgo", drawTetrahedra="0", drawScaleTetrahedra="0.8")
    
    # Set the mechanical parameters and force fields
    bodyMechanics.addObject('UniformMass', totalMass=0.5) # add mass
    bodyMechanics.addObject('TetrahedronFEMForceField', youngModulus=180, poissonRatio=0.45) # add elasticity

    # Define resolution method
    bodyMechanics.addObject('EulerImplicitSolver') # define numerical scheme
    bodyMechanics.addObject('SparseLDLSolver', template="CompressedRowSparseMatrixMat3x3d") # define solve method
    


    # Fix the tail of the larva, so that it is anchored and we can deform the larva by pulling on it
    # bodyMechanics.addObject('BoxROI', name="boxROI", box=[55, -25, -10, 80, 15, 10], drawBoxes=True) # create an anchor or selection zone (red skeleton)
    # bodyMechanics.addObject('FixedConstraint', indices="@boxROI.indices") # add the constraint
    bodyMechanics.addObject('UncoupledConstraintCorrection') # add the constraint solver

    # Set a visual model
    visualModel = larvaBody.addChild('visualModel')
    visualModel.addObject('OglModel', name='visualMesh', src='@../larvaMesh')
    # Align the visual model on the coarse mechanical mesh
    visualModel.addObject('BarycentricMapping', input='@../bodyMechanics/dofs', output='@visualMesh')

    # Collision model
    collision = bodyMechanics.addChild('larvaCollisionModel') # collision model
    collision.addObject('TriangleSetTopologyContainer', name="Container")
    collision.addObject('TriangleSetTopologyModifier')
    collision.addObject('Tetra2TriangleTopologicalMapping', input="@../topo", output="@Container")
    collision.addObject('MechanicalObject', name="tetras", template="Vec3", position="@../gen.outputPoints")    
    collision.addObject('TriangleCollisionModel', selfCollision=True) # 3 types of collision
    collision.addObject('LineCollisionModel', selfCollision=True)
    collision.addObject('PointCollisionModel', selfCollision=True)
    collision.addObject('BarycentricMapping', input="@../dofs")

    
    
    return rootNode

Answered by hugtalbot

Dec 14, 2023

Hi @aleblanc30

I detected several issues in your scene:

the time step you are using is too large. As a consequence, the collision detection had no time to catch any collision
the CollisionHeader() prefab, based on a RuleBasedContactManager for the collision response is not appropriate. We should actually update this prefab.

Let me know if the example below is working for you 👇

import Sofa
from stlib3.scene import ContactHeader
from stlib3.physics.rigid import Floor

# Units : mm and kg

def createScene(rootNode):
    
    rootNode.findData('dt').value = 0.001
    rootNode.findData('gravity').value = [0, 0, -9180] # gravity is disabled
    rootNode.addObject('VisualStyle',
            …

View full answer

aleblanc30 · 2023-12-11T09:53:22Z

aleblanc30
Dec 11, 2023
Author

I updated the collision model according to #4033 :

    collision = bodyMechanics.addChild('larvaCollisionModel') # collision model
    collision.addObject('TriangleSetTopologyContainer', name="Container")#, position="@../topo.position") # uncomment to get a segfault
    collision.addObject('TriangleSetTopologyModifier')
    collision.addObject('Tetra2TriangleTopologicalMapping', input="@../topo", output="@Container")

    collision.addObject('MechanicalObject', name="collisionDOFs")    
    collision.addObject('IdentityMapping', input="@../dofs", output="@collisionDOFs")

    collision.addObject('TriangleCollisionModel', selfCollision=True) # 3 types of collision
    collision.addObject('LineCollisionModel', selfCollision=True)
    collision.addObject('PointCollisionModel', selfCollision=True)

and suddenly the plot thickened, as I got a different buggy behavior : more vertices inside are now considered for collision.

Also, initializing the position attribute of the TriangleSetTopologyContainer now seems crucial to avoid a segfault, and I do not get warnings from Tetra2TriangleTopologyContainer anymore.

0 replies

hugtalbot · 2023-12-12T11:21:46Z

hugtalbot
Dec 12, 2023
Maintainer

Hi @aleblanc30

Thanks a lot for your question.
TopologicalMappings (like the Tetra2TriangleTopologyContainer) are non-mechanical mappings which rely on the degrees of freedom of the mechanical object (in your case the one named dofs). No MechanicaObject should there be added in the subnode of the TopologicalMappings.

In your case, just remove both lines:

    collision.addObject('MechanicalObject', name="collisionDOFs")    
    collision.addObject('IdentityMapping', input="@../dofs", output="@collisionDOFs")

Hope this helps

0 replies

aleblanc30 · 2023-12-12T12:25:46Z

aleblanc30
Dec 12, 2023
Author

Hi @hugtalbot, thank you for your availability.

I followed your recommendation. The behavior is a bit better but I still have issues with collisions only being detected at interior points of the mesh. See the following screenshots :

Collision models:

Bounding boxes and interaction forces : the forces are on the surface of the floor, inside the body.

Collision model and interaction forces, viewed from inside the model : the interaction occurs at isolated points inside the collision model

3 replies

hugtalbot Dec 12, 2023
Maintainer

Do you have a repo which I could test with the scene + files @aleblanc30 ?

aleblanc30 Dec 12, 2023
Author

Here it is : https://github.com/aleblanc30/weird_collisions

aleblanc30 Dec 13, 2023
Author

Following the conversation with @epernod I updated the repo to add a corrected floor mesh with correct normals.

epernod · 2023-12-13T08:40:52Z

epernod
Dec 13, 2023
Maintainer

Hi,
could you check your mesh normal directions. Of both mesh, the floor and your "thing". I'm pretty sure the normal of the floor are going on the inside.

You can display the normal in the default runSofa UI visual options.
You have a Data in the Tetra2TriangleTopologicalMapping to inverse the normals if needed

Hope it helps

1 reply

aleblanc30 Dec 13, 2023
Author

The "thing" is a mesh of a drosophila larva, maybe I should have started with that :-)

I'll check the normals and get back to you

aleblanc30 · 2023-12-13T09:32:31Z

aleblanc30
Dec 13, 2023
Author

Apparently the normals of my mesh are fine. However the normals of the Floor from STLIB are actually tangent to the surface. I'll look for a way to fix this.

EDIT : I found the function updateNormals in MeshLoader, maybe that would do the trick ? I don't know if it is possible to have it called.

6 replies

aleblanc30 Dec 13, 2023
Author

Can you tell me what the syntax should be ?

epernod Dec 13, 2023
Maintainer

Edit: There is only the flip option.
I would suggest you to update your mesh first in blender for example.

aleblanc30 Dec 13, 2023
Author

👍

aleblanc30 Dec 13, 2023
Author

I updated the normals of the floor in blender. I'd like to point that the mesh is distributed with SOFA in share/sofa/mesh/floor.obj.
The normals are now all pointing outwards, but the issue remains. I really think the fact that the Tetra2TriangleTopologicalMapping leaves isolated vertices inside the mesh is the key problem. At this point I could maybe use CGAL separately to create the mesh, and create manually the corresponding surface mesh for collision detection in order to move forward. It's just that it bothers me that it's not working.

hugtalbot Dec 14, 2023
Maintainer

I am myself compiling the CGAL plugin to test your exact scene and I get back to you afterwards

hugtalbot · 2023-12-14T07:36:16Z

hugtalbot
Dec 14, 2023
Maintainer

Hi @aleblanc30

I detected several issues in your scene:

the time step you are using is too large. As a consequence, the collision detection had no time to catch any collision
the CollisionHeader() prefab, based on a RuleBasedContactManager for the collision response is not appropriate. We should actually update this prefab.

Let me know if the example below is working for you 👇

import Sofa
from stlib3.scene import ContactHeader
from stlib3.physics.rigid import Floor

# Units : mm and kg

def createScene(rootNode):
    
    rootNode.findData('dt').value = 0.001
    rootNode.findData('gravity').value = [0, 0, -9180] # gravity is disabled
    rootNode.addObject('VisualStyle',
                       displayFlags='showCollision hideVisualModels hideForceFields hideInteractionForceFields'
                                     +' hideCollisionModels hideBoundingCollisionModels showWireframe')
    
    rootNode.bbox = "-50 -50 -50 50 50 50" # field of view of the viewer

    # Required plugins
    rootNode.addObject('RequiredPlugin', pluginName=[
                            "Sofa.Component.AnimationLoop",  # Needed to use components FreeMotionAnimationLoop
                            "Sofa.Component.Constraint.Lagrangian.Correction", # Needed to use components LinearSolverConstraintCorrection
                            "Sofa.Component.Constraint.Lagrangian.Solver",  # Needed to use components GenericConstraintSolver
                            "Sofa.Component.Constraint.Projective",  # Needed to use components FixedConstraint
                            "Sofa.Component.Engine.Select",  # Needed to use components BoxROI
                            "Sofa.Component.IO.Mesh",  # Needed to use components MeshVTKLoader
                            "Sofa.Component.LinearSolver.Direct",  # Needed to use components SparseLDLSolver
                            "Sofa.Component.LinearSolver.Iterative",  # Needed to use components ShewchukPCGLinearSolver
                            "Sofa.Component.Mass",  # Needed to use components UniformMass
                            "Sofa.Component.ODESolver.Backward",  # Needed to use components EulerImplicitSolver
                            "Sofa.Component.SolidMechanics.FEM.Elastic",  # Needed to use components TetrahedronFEMForceField
                            "Sofa.Component.Topology.Container.Constant",  # Needed to use components MeshTopology
                            "Sofa.Component.Visual",  # Needed to use components VisualStyle
                            "Sofa.Component.Mapping.Linear", # Needed to use components BarycentricMapping  
                            "Sofa.Component.StateContainer", # Needed to use components MechanicalObject
                            "Sofa.Component.Setting", # Needed to use components BackgroundSetting  
                            "Sofa.Component.Topology.Container.Dynamic", # Needed to use components TetrahedronSetGeometryAlgorithms,TetrahedronSetTopologyContainer  
                            "Sofa.GL.Component.Rendering3D", # Needed to use components OglModel,OglSceneFrame
                            "CGALPlugin",
                            "Sofa.Component.Collision.Detection.Algorithm",
                            "Sofa.Component.Collision.Detection.Intersection",
                            "SofaPython3"
                        ])
    
    rootNode.addObject('BackgroundSetting', color=[0, 0.168627, 0.211765, 1]) # set background color
    rootNode.addObject('OglSceneFrame', style="Arrows", alignment="TopRight") # add a triedron to help with orientation

    # setup the animation loop
    rootNode.addObject('FreeMotionAnimationLoop')
    rootNode.addObject('GenericConstraintSolver', maxIterations=500, tolerance=1e-8)

    # add a collision pipeline
    rootNode.addObject('CollisionPipeline')
    rootNode.addObject('BruteForceBroadPhase')
    rootNode.addObject('BVHNarrowPhase')
    rootNode.addObject('LocalMinDistance',
                        alarmDistance=0.5, contactDistance=0.1,
                        angleCone=0.5)
    rootNode.addObject('CollisionResponse', response='FrictionContactConstraint')

    # Add a floor
    Floor(rootNode, rotation=[90, 0, 0], translation=[0,0,-10], isAStaticObject=True)

    # create the larva object
    larvaBody = rootNode.addChild('larvaBody')

    # load the detailed mesh
    larvaSTL = 'mesh_cuticle_simplified.stl'
    larvaBody.addObject('MeshSTLLoader', name='larvaMesh', filename=larvaSTL)
    
    # create the overall body mechanics
    bodyMechanics = larvaBody.addChild('bodyMechanics')
    
    # use CGAL to create a simplified tetrahedral mesh of the larva
    bodyMechanics.addObject('MeshGenerationFromPolyhedron', name='gen', template='Vec3d', inputPoints='@../larvaMesh.position', inputTriangles='@../larvaMesh.triangles', drawTetras='0',
                       cellSize="10", facetAngle="30", facetSize="5", cellRatio="2",   #Convergence problem if lower than 2
                       facetApproximation="1")
    
    # Create the state from the coarse mesh
    bodyMechanics.addObject('MechanicalObject', name="dofs", position="@gen.outputPoints")
    bodyMechanics.addObject('TetrahedronSetTopologyContainer', name='topo', tetrahedra='@gen.outputTetras')
    bodyMechanics.addObject('TetrahedronSetGeometryAlgorithms', template="Vec3d", name="GeomAlgo", drawTetrahedra="0", drawScaleTetrahedra="0.8")
    
    # Set the mechanical parameters and force fields
    bodyMechanics.addObject('UniformMass', totalMass=0.5) # add mass
    bodyMechanics.addObject('TetrahedronFEMForceField', youngModulus=180, poissonRatio=0.45) # add elasticity

    # Define resolution method
    bodyMechanics.addObject('EulerImplicitSolver') # define numerical scheme
    bodyMechanics.addObject('SparseLDLSolver', template="CompressedRowSparseMatrixMat3x3d") # define solve method
    


    # Fix the tail of the larva, so that it is anchored and we can deform the larva by pulling on it
    # bodyMechanics.addObject('BoxROI', name="boxROI", box=[55, -25, -10, 80, 15, 10], drawBoxes=True) # create an anchor or selection zone (red skeleton)
    # bodyMechanics.addObject('FixedConstraint', indices="@boxROI.indices") # add the constraint
    bodyMechanics.addObject('UncoupledConstraintCorrection') # add the constraint solver

    # Set a visual model
    visualModel = larvaBody.addChild('visualModel')
    visualModel.addObject('OglModel', name='visualMesh', src='@../larvaMesh')
    # Align the visual model on the coarse mechanical mesh
    visualModel.addObject('BarycentricMapping', input='@../bodyMechanics/dofs', output='@visualMesh')

    # Collision model
    collision = bodyMechanics.addChild('larvaCollisionModel') # collision model
    collision.addObject('TriangleSetTopologyContainer', name="Container")
    collision.addObject('TriangleSetTopologyModifier')
    collision.addObject('Tetra2TriangleTopologicalMapping', input="@../topo", output="@Container")

    collision.addObject('TriangleCollisionModel', selfCollision=True) # 3 types of collision
    collision.addObject('LineCollisionModel', selfCollision=True)
    collision.addObject('PointCollisionModel', selfCollision=True)
    
    
    return rootNode

Cheers

2 replies

aleblanc30 Dec 14, 2023
Author

It works just fine, thank you so much !

hugtalbot Dec 14, 2023
Maintainer

You're very welcome @aleblanc30 🙌

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Issue with collisions, possibly related to CGAL plugin and/or Tetra2TriangleTopologicalMapping #4346

aleblanc30 Dec 11, 2023

Replies: 6 comments · 12 replies

aleblanc30 Dec 11, 2023 Author

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