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Sofa cgal tetrahedron push with repulsive force #4

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89860d5
[Intersection Push] Adding Repulsive Force Field using tetrahedron me…
FadiWahbeh Jul 9, 2026
803071b
Update scene to use a RestShapeSpringFF as boundary condition
epernod Jul 9, 2026
7ea8d2a
[scenes] Add node to map collision obj mesh. Also add MeshExporter bu…
epernod Jul 10, 2026
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120 changes: 120 additions & 0 deletions scenes/MeshRepulsion_patient_01.scn
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<?xml version="1.0"?>
<!-- =========================================================================
PR08 : CGAL detection -> standard SOFA RepulsiveSpringForceField

Goal:
- CGAL detects inside vertices and edge/face crossings.
- CGAL builds spring pairs only every N steps.
- The standard SOFA RepulsiveSpringForceField applies the mechanical force.
- The master AABB tree is built once by default; it is not rebuilt at each step.

Objects:
- liver_coarse.msh = MASTER, fixed.
- diaphragm.msh = SLAVE 1, tetra volume + mapped contact surface.
- bone.msh = SLAVE 2, triangle-only surface fallback.

No translation / rotation / scale is applied.
========================================================================= -->
<Node name="root" gravity="0 0 0" dt="0.003">
<RequiredPlugin pluginName="Sofa.Component.AnimationLoop"/>
<RequiredPlugin pluginName="Sofa.Component.IO.Mesh"/>
<RequiredPlugin pluginName="Sofa.Component.Mapping.Linear"/>
<RequiredPlugin pluginName="Sofa.Component.Setting"/>
<RequiredPlugin pluginName="Sofa.Component.StateContainer"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Container.Constant"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Container.Dynamic"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Mapping"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Utility"/>
<RequiredPlugin pluginName="Sofa.Component.Visual"/>
<RequiredPlugin pluginName="Sofa.GL.Component.Rendering3D"/>
<RequiredPlugin pluginName="Sofa.Component.LinearSolver.Iterative"/>
<RequiredPlugin pluginName="Sofa.Component.Mass"/>
<RequiredPlugin pluginName="Sofa.Component.ODESolver.Backward"/>
<RequiredPlugin pluginName="Sofa.Component.SolidMechanics.FEM.Elastic"/>
<RequiredPlugin pluginName="Sofa.Component.SolidMechanics.Spring"/>
<RequiredPlugin pluginName="CGALPlugin"/>

<BackgroundSetting color="0 0.16862745098 0.21176470588"/>
<VisualStyle displayFlags="showVisualModels showBehaviorModels"/>
<DefaultAnimationLoop/>

<Node name="MasterLiver">
<MeshGmshLoader name="loader" filename="./STL_Intersection_Objects/Patient_01/liver_coarse_patient_01.msh"/>
<MechanicalObject name="dofs" template="Vec3d" position="@loader.position" showObject="false"/>
<TriangleSetTopologyContainer name="topology" src="@loader"/>
<TriangleSetTopologyModifier name="topologyModifier"/>
<TriangleSetGeometryAlgorithms name="geometryAlgorithms" template="Vec3d"/>

<Node name="Visual">
<OglModel name="visu" src="@../loader" color="1 0.05 0.05 1.0"/>
<IdentityMapping input="@../dofs" output="@visu"/>
</Node>
</Node>

<Node name="SlaveDiaphragmVolume">
<EulerImplicitSolver name="odesolver" rayleighStiffness="0.25" rayleighMass="0.45"/>
<CGLinearSolver name="linearsolver" iterations="60" tolerance="1.0e-6" threshold="1.0e-6"/>

<MeshGmshLoader name="volumeLoader" filename="./STL_Intersection_Objects/Patient_01/diaphragm_patient_01.msh"/>
<MechanicalObject name="dofs" template="Vec3d" position="@volumeLoader.position" showObject="false"/>
<TetrahedronSetTopologyContainer name="topology" src="@volumeLoader"/>
<TetrahedronSetTopologyModifier name="topologyModifier"/>
<TetrahedronSetGeometryAlgorithms name="geometryAlgorithms" template="Vec3d"/>

<!-- to adapt to the scene -->
<!--
<BoxROI name="box_roi" box="0 0 0 300 300 70 0 0 220 300 300 300" drawBoxes="1"/>
<FixedProjectiveConstraint indices="@[-1].indices" />
-->
<UniformMass totalMass="1.2"/>
<TetrahedronFEMForceField name="tetraFEM" template="Vec3d" method="large" youngModulus="5000" poissonRatio="0.45"/>

<RestShapeSpringsForceField stiffness="100" angularStiffness="100" />


<Node name="ContactSurface">
<MechanicalObject name="surfaceDofs" template="Vec3d" position="@../volumeLoader.position" showObject="false"/>
<TriangleSetTopologyContainer name="surfaceTopology" src="@../volumeLoader"/>
<TriangleSetTopologyModifier name="surfaceTopologyModifier"/>
<TriangleSetGeometryAlgorithms name="surfaceGeometryAlgorithms" template="Vec3d"/>
<BarycentricMapping name="surfaceToVolumeMapping" input="@../dofs" output="@surfaceDofs" mapForces="true" mapMasses="false"/>

<MeshRepulsionEngine name="diaphragmCgalSpringPairs" template="Vec3d"
masterState="@../../MasterLiver/dofs"
masterTopology="@../../MasterLiver/topology"
slaveState="@surfaceDofs"
slaveTopology="@surfaceTopology"
repulsiveSpringField="@diaphragmRepulsiveSprings"
safetyDistance="1.2"
crossingDepth="2.2"
pushInsideVertices="true"
pushEdgeCrossings="true"
pushFaceCrossings="false"
rebuildMasterEveryStep="false"
computeEveryNSteps="4"
maxPairs="2500"
maxEdgesCheckedPerUpdate="8000"
maxFacesCheckedPerUpdate="0"
logEveryNSteps="20"
stiffness="10000"
maxForce="10000"
/>

<Node name="Visual">
<OglModel name="visu" src="@../../volumeLoader" color="0.15 0.55 1.0 0.35"/>
<IdentityMapping input="@../surfaceDofs" output="@visu"/>
</Node>

<Node name="CollisionMesh">
<MeshOBJLoader name="loader_surface" filename="./STL_Intersection_Objects/Patient_01/diaphragm_patient_01.obj"/>
<MechanicalObject name="collisionDofs" template="Vec3d" position="@loader_surface.position"/>
<TriangleSetTopologyContainer name="collisionTopology" src="@loader_surface"/>
<TriangleSetTopologyModifier name="collisionTopologyModifier"/>
<TriangleSetGeometryAlgorithms name="collisionGeometryAlgorithms" template="Vec3d" drawEdges="1"/>
<BarycentricMapping input="@../surfaceDofs" output="@collisionDofs"/>
<MeshExporter triangles="@collisionTopology.triangles" edges="@collisionTopology.edges" position="@collisionDofs.position" exportAtEnd="1" filename="toto.obj"/>
</Node>

</Node>
</Node>
</Node>
91 changes: 91 additions & 0 deletions scenes/MeshRepulsion_patient_08.scn
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<?xml version="1.0"?>
<!-- =========================================================================
PR08 : CGAL detection -> standard SOFA RepulsiveSpringForceField
Patient 16. Master = liver (.obj). Slave = diaphragm tetra.
No translation / rotation / scale is applied.
========================================================================= -->
<Node name="root" gravity="0 0 0" dt="0.003">
<RequiredPlugin pluginName="Sofa.Component.AnimationLoop"/>
<RequiredPlugin pluginName="Sofa.Component.IO.Mesh"/>
<RequiredPlugin pluginName="Sofa.Component.Mapping.Linear"/>
<RequiredPlugin pluginName="Sofa.Component.Setting"/>
<RequiredPlugin pluginName="Sofa.Component.StateContainer"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Container.Constant"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Container.Dynamic"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Mapping"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Utility"/>
<RequiredPlugin pluginName="Sofa.Component.Visual"/>
<RequiredPlugin pluginName="Sofa.GL.Component.Rendering3D"/>
<RequiredPlugin pluginName="Sofa.Component.LinearSolver.Iterative"/>
<RequiredPlugin pluginName="Sofa.Component.Mass"/>
<RequiredPlugin pluginName="Sofa.Component.ODESolver.Backward"/>
<RequiredPlugin pluginName="Sofa.Component.SolidMechanics.FEM.Elastic"/>
<RequiredPlugin pluginName="Sofa.Component.SolidMechanics.Spring"/>
<RequiredPlugin pluginName="CGALPlugin"/>

<BackgroundSetting color="0 0.16862745098 0.21176470588"/>
<VisualStyle displayFlags="showVisualModels"/>
<DefaultAnimationLoop/>

<Node name="MasterLiver">
<MeshOBJLoader name="loader" filename="./STL_Intersection_Objects/Patient_08/liver_coarse_patient_08.msh"/>
<MechanicalObject name="dofs" template="Vec3d" position="@loader.position" showObject="false"/>
<TriangleSetTopologyContainer name="topology" src="@loader"/>
<TriangleSetTopologyModifier name="topologyModifier"/>
<TriangleSetGeometryAlgorithms name="geometryAlgorithms" template="Vec3d"/>

<Node name="Visual">
<OglModel name="visu" src="@../loader" color="1 0.05 0.05 1.0"/>
<IdentityMapping input="@../dofs" output="@visu"/>
</Node>
</Node>

<Node name="SlaveDiaphragmVolume">
<EulerImplicitSolver name="odesolver" rayleighStiffness="0.25" rayleighMass="0.45"/>
<CGLinearSolver name="linearsolver" iterations="60" tolerance="1.0e-6" threshold="1.0e-6"/>

<MeshGmshLoader name="volumeLoader" filename="./STL_Intersection_Objects/Patient_08/diaphragm_patient_08.msh"/>
<MechanicalObject name="dofs" template="Vec3d" position="@volumeLoader.position" showObject="false"/>
<TetrahedronSetTopologyContainer name="topology" src="@volumeLoader"/>
<TetrahedronSetTopologyModifier name="topologyModifier"/>
<TetrahedronSetGeometryAlgorithms name="geometryAlgorithms" template="Vec3d"/>

<UniformMass totalMass="1.2"/>
<TetrahedronFEMForceField name="tetraFEM" template="Vec3d" method="large" youngModulus="5000" poissonRatio="0.45"/>
<RestShapeSpringsForceField stiffness="100" angularStiffness="100" />

<Node name="ContactSurface">
<MechanicalObject name="surfaceDofs" template="Vec3d" position="@../volumeLoader.position" showObject="false"/>
<TriangleSetTopologyContainer name="surfaceTopology" src="@../volumeLoader"/>
<TriangleSetTopologyModifier name="surfaceTopologyModifier"/>
<TriangleSetGeometryAlgorithms name="surfaceGeometryAlgorithms" template="Vec3d"/>
<BarycentricMapping name="surfaceToVolumeMapping" input="@../dofs" output="@surfaceDofs" mapForces="true" mapMasses="false"/>

<MeshRepulsionEngine name="diaphragmCgalSpringPairs" template="Vec3d"
masterState="@../../MasterLiver/dofs"
masterTopology="@../../MasterLiver/topology"
slaveState="@surfaceDofs"
slaveTopology="@surfaceTopology"
repulsiveSpringField="@diaphragmRepulsiveSprings"
safetyDistance="1.2"
crossingDepth="2.2"
pushInsideVertices="true"
pushEdgeCrossings="true"
pushFaceCrossings="true"
rebuildMasterEveryStep="false"
computeEveryNSteps="4"
maxPairs="2500"
maxEdgesCheckedPerUpdate="8000"
maxFacesCheckedPerUpdate="0"
logEveryNSteps="20"
stiffness="10000"
maxForce="10000"
/>

<Node name="Visual">
<OglModel name="visu" src="@../../volumeLoader" color="0.15 0.55 1.0 0.35"/>
<IdentityMapping input="@../surfaceDofs" output="@visu"/>
</Node>
</Node>
</Node>
</Node>
91 changes: 91 additions & 0 deletions scenes/MeshRepulsion_patient_16.scn
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Original file line number Diff line number Diff line change
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<?xml version="1.0"?>
<!-- =========================================================================
PR08 : CGAL detection -> standard SOFA RepulsiveSpringForceField
Patient 08. Master = liver (.msh, surface used). Slave = diaphragm tetra.
No translation / rotation / scale is applied.
========================================================================= -->
<Node name="root" gravity="0 0 0" dt="0.003">
<RequiredPlugin pluginName="Sofa.Component.AnimationLoop"/>
<RequiredPlugin pluginName="Sofa.Component.IO.Mesh"/>
<RequiredPlugin pluginName="Sofa.Component.Mapping.Linear"/>
<RequiredPlugin pluginName="Sofa.Component.Setting"/>
<RequiredPlugin pluginName="Sofa.Component.StateContainer"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Container.Constant"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Container.Dynamic"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Mapping"/>
<RequiredPlugin pluginName="Sofa.Component.Topology.Utility"/>
<RequiredPlugin pluginName="Sofa.Component.Visual"/>
<RequiredPlugin pluginName="Sofa.GL.Component.Rendering3D"/>
<RequiredPlugin pluginName="Sofa.Component.LinearSolver.Iterative"/>
<RequiredPlugin pluginName="Sofa.Component.Mass"/>
<RequiredPlugin pluginName="Sofa.Component.ODESolver.Backward"/>
<RequiredPlugin pluginName="Sofa.Component.SolidMechanics.FEM.Elastic"/>
<RequiredPlugin pluginName="Sofa.Component.SolidMechanics.Spring"/>
<RequiredPlugin pluginName="CGALPlugin"/>

<BackgroundSetting color="0 0.16862745098 0.21176470588"/>
<VisualStyle displayFlags="showVisualModels"/>
<DefaultAnimationLoop/>

<Node name="MasterLiver">
<MeshGmshLoader name="loader" filename="./STL_Intersection_Objects/Patient_16/liver_coarse_patient_16.msh"/>
<MechanicalObject name="dofs" template="Vec3d" position="@loader.position" showObject="false"/>
<TriangleSetTopologyContainer name="topology" src="@loader"/>
<TriangleSetTopologyModifier name="topologyModifier"/>
<TriangleSetGeometryAlgorithms name="geometryAlgorithms" template="Vec3d"/>

<Node name="Visual">
<OglModel name="visu" src="@../loader" color="1 0.05 0.05 1.0"/>
<IdentityMapping input="@../dofs" output="@visu"/>
</Node>
</Node>

<Node name="SlaveDiaphragmVolume">
<EulerImplicitSolver name="odesolver" rayleighStiffness="0.25" rayleighMass="0.45"/>
<CGLinearSolver name="linearsolver" iterations="60" tolerance="1.0e-6" threshold="1.0e-6"/>

<MeshGmshLoader name="volumeLoader" filename="./STL_Intersection_Objects/Patient_16/diaphragm_patient_16.msh"/>
<MechanicalObject name="dofs" template="Vec3d" position="@volumeLoader.position" showObject="false"/>
<TetrahedronSetTopologyContainer name="topology" src="@volumeLoader"/>
<TetrahedronSetTopologyModifier name="topologyModifier"/>
<TetrahedronSetGeometryAlgorithms name="geometryAlgorithms" template="Vec3d"/>

<UniformMass totalMass="1.2"/>
<TetrahedronFEMForceField name="tetraFEM" template="Vec3d" method="large" youngModulus="5000" poissonRatio="0.45"/>
<RestShapeSpringsForceField stiffness="100" angularStiffness="100" />

<Node name="ContactSurface">
<MechanicalObject name="surfaceDofs" template="Vec3d" position="@../volumeLoader.position" showObject="false"/>
<TriangleSetTopologyContainer name="surfaceTopology" src="@../volumeLoader"/>
<TriangleSetTopologyModifier name="surfaceTopologyModifier"/>
<TriangleSetGeometryAlgorithms name="surfaceGeometryAlgorithms" template="Vec3d"/>
<BarycentricMapping name="surfaceToVolumeMapping" input="@../dofs" output="@surfaceDofs" mapForces="true" mapMasses="false"/>

<MeshRepulsionEngine name="diaphragmCgalSpringPairs" template="Vec3d"
masterState="@../../MasterLiver/dofs"
masterTopology="@../../MasterLiver/topology"
slaveState="@surfaceDofs"
slaveTopology="@surfaceTopology"
repulsiveSpringField="@diaphragmRepulsiveSprings"
safetyDistance="1.2"
crossingDepth="2.2"
pushInsideVertices="true"
pushEdgeCrossings="true"
pushFaceCrossings="false"
rebuildMasterEveryStep="false"
computeEveryNSteps="4"
maxPairs="2500"
maxEdgesCheckedPerUpdate="8000"
maxFacesCheckedPerUpdate="0"
logEveryNSteps="20"
stiffness="10000"
maxForce="10000"
/>

<Node name="Visual">
<OglModel name="visu" src="@../../volumeLoader" color="0.15 0.55 1.0 0.35"/>
<IdentityMapping input="@../surfaceDofs" output="@visu"/>
</Node>
</Node>
</Node>
</Node>
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