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alxbilger merged 8 commits into from
May 6, 2025
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[Examples] Clean xml examples from folder combo/miccai2013 #11

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7f3759b
[examples] Update scene
Apr 11, 2025
f908a4b
clean example from folder xml/combo
Apr 24, 2025
e12b219
fix paths 200shellComputationAnevrism
Apr 24, 2025
1fed94f
remove comments + move LCPConstraintSolver
Apr 25, 2025
d0dcb2a
clean examples 30/04
Apr 30, 2025
304af46
fix last commit
May 5, 2025
5203979
Delete doc/Vrst2013/vrst2013.pdf
Lucas-TJ May 6, 2025
9ef2386
Delete doc/VRIPHYS2012/vriphys2012.pdf
Lucas-TJ May 6, 2025
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52 changes: 40 additions & 12 deletions examples/xml/200shellComputationAnevrism.scn
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Original file line number Diff line number Diff line change
@@ -1,5 +1,28 @@
<?xml version="1.0" ?>

<Node name="root" dt="0.04" gravity="0 -10 0">
<!-- List of plugins needed to load all components used by this scene -->
<Node name="plugins">
<RequiredPlugin name="Sofa.Component.AnimationLoop"/> <!-- Needed to use components [FreeMotionAnimationLoop] -->
<RequiredPlugin name="Sofa.Component.Constraint.Projective"/> <!-- Needed to use components [FixedProjectiveConstraint,FixedRotationProjectiveConstraint] -->
<RequiredPlugin name="Sofa.Component.Constraint.Lagrangian.Solver"/> <!-- Needed to use components [LCPConstraintSolver] -->
<RequiredPlugin name="Sofa.Component.Engine.Select"/> <!-- Needed to use components [BoxROI] -->
<RequiredPlugin name="Sofa.Component.Engine.Transform"/> <!-- Needed to use components [Vertex2Frame] -->
<RequiredPlugin name="Sofa.Component.LinearSolver.Direct"/> <!-- Needed to use components [SparseLDLSolver] -->
<RequiredPlugin name="Sofa.Component.LinearSolver.Iterative"/> <!-- Needed to use components [PCGLinearSolver] -->
<RequiredPlugin name="Sofa.Component.Mapping.Linear"/> <!-- Needed to use components [IdentityMapping] -->
<RequiredPlugin name="Sofa.Component.Mass"/> <!-- Needed to use components [UniformMass] -->
<RequiredPlugin name="Sofa.Component.ODESolver.Backward"/> <!-- Needed to use components [EulerImplicitSolver] -->
<RequiredPlugin name="Sofa.Component.SceneUtility"/> <!-- Needed to use components [InfoComponent] -->
<RequiredPlugin name="Sofa.Component.StateContainer"/> <!-- Needed to use components [MechanicalObject] -->
<RequiredPlugin name="Sofa.Component.Topology.Container.Dynamic"/> <!-- Needed to use components [TriangleSetTopologyContainer] -->
<RequiredPlugin name="Sofa.Component.Visual"/> <!-- Needed to use components [VisualStyle] -->
<RequiredPlugin name="Sofa.Component.IO.Mesh"/> <!-- Needed to use components [MeshOBJLoader] -->
<RequiredPlugin name="Sofa.GL.Component.Rendering3D"/> <!-- Needed to use components [OglModel] -->
<RequiredPlugin name="Shell"/>
</Node>



<VisualStyle displayFlags="showForceFields showVisualModels" />

Expand All @@ -9,15 +32,21 @@
<!-- <MinProximityIntersection name="Proximity" alarmDistance="0.8" contactDistance="0.5" />-->
<!-- <CollisionGroup />-->


<!--<DefaultAnimationLoop/>-->

<FreeMotionAnimationLoop computeBoundingBox="true"/>
<LCPConstraintSolver/>

<Node name="CoarseMesh">
<MeshObjLoader name="coarseMesh" filename="../mesh/aneurysm200.obj"/>
<Vertex2Frame name="coarseMeshVertex2Frame" template="Rigid" position="@coarseMesh.position" normals="@coarseMesh.normals" invertNormals="false"/>
<MeshOBJLoader name="coarseMesh" filename="../../../Shell/mesh/aneurysm200.obj"/>
<Vertex2Frame name="coarseMeshVertex2Frame" template="Rigid3" position="@coarseMesh.position" normals="@coarseMesh.normals" invertNormals="false"/>

</Node>


<Node name="TargetMesh">
<MeshObjLoader name="targetMesh" filename="../mesh/aneurysmHighRes.obj"/>
<MeshOBJLoader name="targetMesh" filename="../../../Shell/mesh/aneurysmHighRes.obj"/>
<TriangleSetTopologyContainer name="targetTopo" src="@targetMesh" />
<!-- <MechanicalObject name="targetMesh_MO" template="Vec3d"/> -->
</Node>
Expand All @@ -27,22 +56,21 @@
<Node name="Shell">
<EulerImplicitSolver />
<!--<CGLinearSolver iterations="20" tolerance="0.05" threshold="1e-20"/>-->

<PCGLinearSolver iterations="5" tolerance="0.05" preconditioners="Precond"/>
<SparseLDLSolver name="Precond"/>
<PCGLinearSolver iterations="5" tolerance="0.05" preconditioner="@Precond"/>
<SparseLDLSolver name="Precond" template="CompressedRowSparseMatrixMat3x3"/>


<TriangleSetTopologyContainer name="coarseTopo"
position="@/CoarseMesh/coarseMesh.position"
edges="@/CoarseMesh/coarseMesh.edges"
triangles="@/CoarseMesh/coarseMesh.triangles" />
<MechanicalObject name="coarseMesh_MO" template="Rigid" rest_position="@/CoarseMesh/coarseMeshVertex2Frame.frames" position="@/CoarseMesh/coarseMeshVertex2Frame.frames"/>
<MechanicalObject name="coarseMesh_MO" template="Rigid3d" rest_position="@/CoarseMesh/coarseMeshVertex2Frame.frames" position="@/CoarseMesh/coarseMeshVertex2Frame.frames"/>

<UniformMass mass="0.3 0.1 [ 0.1 0 0 , 0 0.1 0 , 0 0 0.05 ]" showAxisSizeFactor="0.03" compute_mapping_inertia="0" />
<UniformMass vertexMass="0.3 0.1 [ 0.1 0 0 , 0 0.1 0 , 0 0 0.05 ]" showAxisSizeFactor="0.03" compute_mapping_inertia="0" totalMass="1.0" />

<BoxConstraint box="-0.2 -1 -0.2 0.2 -0.8 0.2 0.4 0.3 -0.8 0.8 0.7 -0.7" />

<FixedRotationConstraint FixedZRotation="true" />
<FixedRotationProjectiveConstraint template ="Rigid3" FixedZRotation="true" />
<TriangularBendingFEMForceField name="FEM" bending="true"
youngModulus="5000000" poissonRatio="0.45" thickness="0.05" />

Expand All @@ -53,11 +81,11 @@
<TriangleSetTopologyContainer name="subTrianglesTopo"
position="@/TargetMesh/targetTopo.position" triangles="@/TargetMesh/targetTopo.triangles" />
<MechanicalObject name="subCoarse_MO" rest_position="@/TargetMesh/targetTopo.position" />
<BendingPlateMechanicalMapping printLog="1" object1="coarseMesh_MO" object2="subCoarse_MO" name="MappingShells" isMechanical="false"/>
<BendingPlateMechanicalMapping printLog="1" input="@../coarseMesh_MO" output="@subCoarse_MO" name="MappingShells" isMechanical="false"/>

<Node>
<Node name="Visu">
<OglModel name="Visual" color="red"/>
<IdentityMapping object1="subCoarse_MO" object2="Visual"/>
<IdentityMapping input="@../subCoarse_MO" output="@Visual"/>
</Node>
</Node>

Expand Down
94 changes: 62 additions & 32 deletions examples/xml/combo/miccai2013/Aspiration-dual.scn
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Original file line number Diff line number Diff line change
Expand Up @@ -15,22 +15,52 @@
-->

<Node name="root" dt="0.01" gravity="0 0 0">


<Node name="plugins">
<RequiredPlugin name="MultiThreading"/> <!-- Needed to use components [ParallelBVHNarrowPhase,ParallelBruteForceBroadPhase] -->
<RequiredPlugin name="Sofa.Component.AnimationLoop"/> <!-- Needed to use components [FreeMotionAnimationLoop] -->
<RequiredPlugin name="Sofa.Component.Collision.Detection.Algorithm"/> <!-- Needed to use components [BVHNarrowPhase,BruteForceBroadPhase,BruteForceDetection,CollisionPipeline] -->
<RequiredPlugin name="Sofa.Component.Collision.Detection.Intersection"/> <!-- Needed to use components [LocalMinDistance] -->
<RequiredPlugin name="Sofa.Component.Constraint.Lagrangian.Correction"/> <!-- Needed to use components [LinearSolverConstraintCorrection] -->
<RequiredPlugin name="Sofa.Component.Constraint.Lagrangian.Solver"/> <!-- Needed to use components [GenericConstraintSolver] -->
<RequiredPlugin name="Sofa.Component.Constraint.Projective"/> <!-- Needed to use components [FixedProjectiveConstraint] -->
<RequiredPlugin name="Sofa.Component.Engine.Select"/> <!-- Needed to use components [BoxROI,SphereROI] -->
<RequiredPlugin name="Sofa.Component.IO.Mesh"/> <!-- Needed to use components [MeshSTLLoader,MeshVTKLoader,VTKExporter] -->
<RequiredPlugin name="Sofa.Component.LinearSolver.Direct"/> <!-- Needed to use components [SparseLDLSolver template="CompressedRowSparseMatrixMat3x3d"] -->
<RequiredPlugin name="Sofa.Component.Mapping.Linear"/> <!-- Needed to use components [BarycentricMapping,IdentityMapping] -->
<RequiredPlugin name="Sofa.Component.Mass"/> <!-- Needed to use components [UniformMass] -->
<RequiredPlugin name="Sofa.Component.MechanicalLoad"/> <!-- Needed to use components [SurfacePressureForceField] -->
<RequiredPlugin name="Sofa.Component.SceneUtility"/> <!-- Needed to use components [InfoComponent] -->
<RequiredPlugin name="Sofa.Component.SolidMechanics.FEM.Elastic"/> <!-- Needed to use components [TetrahedronFEMForceField] -->
<RequiredPlugin name="Sofa.Component.StateContainer"/> <!-- Needed to use components [MechanicalObject] -->
<RequiredPlugin name="Sofa.Component.Topology.Container.Dynamic"/> <!-- Needed to use components [TetrahedronSetTopologyContainer,TriangleSetTopologyContainer,TriangleSetTopologyModifier] -->
<RequiredPlugin name="Sofa.Component.Topology.Mapping"/> <!-- Needed to use components [Tetra2TriangleTopologicalMapping] -->
<RequiredPlugin name="Sofa.Component.Visual"/> <!-- Needed to use components [VisualStyle] -->
<RequiredPlugin name="Sofa.GL.Component.Rendering3D"/> <!-- Needed to use components [OglModel] -->
<RequiredPlugin name='Sofa.Component.Collision.Response.Contact'/>
<RequiredPlugin name="Sofa.Component.Collision.Geometry"/> <!-- Needed to use components [LineCollisionModel] -->
<RequiredPlugin name="Sofa.Component.ODESolver.Backward"/> <!-- Needed to use components [EulerImplicitSolver] -->
<RequiredPlugin name="Sofa.Component.Topology.Container.Constant"/> <!-- Needed to use components [MeshTopology] -->
<RequiredPlugin name="Shell"/>
</Node>


<VisualStyle displayFlags="showVisual hideForceFields hideCollisionModels" />

<FreeMotionAnimationLoop />
<GenericConstraintSolver tolerance="1e-8" printLog="false"/>
<!--<ComplianceVisualModel />-->
<FreeMotionAnimationLoop />
<LCPConstraintSolver maxIt="1000" tolerance="1e-8" printLog="false"/>
<CollisionPipeline depth="6" verbose="0" draw="0"/>
<BruteForceDetection name="N2" />
<!--<MinProximityIntersection name="proximity" alarmDistance="0.1" contactDistance="0.01" />-->
<LocalMinDistance name="Proximity" alarmDistance="0.01" contactDistance="0.0005" angleCone="0.0" />
<DefaultContactManager name="Response" response="FrictionContact" />
<ParallelBruteForceBroadPhase name="N2"/>
<ParallelBVHNarrowPhase/>
<LocalMinDistance name="Proximity" alarmDistance="0.01" contactDistance="0.0005" angleCone="0.0" />
<CollisionResponse name="Response" response="FrictionContactConstraint" />

<Node name="VolMesh">
<!--<MeshVTKLoader name="loader" filename="../cube2739.vtk"-->
<MeshVTKLoader name="loader" filename="cube2648G.vtk"
scale3d="0.015 0.015 0.015" translation="-0.0075 0 -0.0075" />
<TetrahedronSetTopologyContainer name="topo" src="@loader" />
<TetrahedronSetTopologyContainer name="topo" triangles="@loader.triangles" position="@loader.position" />
<MechanicalObject name="VolMO" />
<Node name="Surface">
<TriangleSetTopologyContainer name="triangles" />
Expand All @@ -41,33 +71,33 @@
</Node>

<Node name="SurfMesh">
<!--<MeshObjLoader name="loader" filename="../cube2739.obj"-->
<MeshObjLoader name="loader" filename="cube2648G.obj"
<!--<MeshOBJLoader name="loader" filename="../cube2739.obj"-->
<MeshOBJLoader name="loader" filename="cube2648G.obj"
scale3d="0.015 0.015 0.015" translation="-0.0075 0 -0.0075" />
<TriangleSetTopologyContainer name="topo" src="@loader" />
<MechanicalObject name="SurfMO" />
</Node>

<Node name="TubeMesh">
<MeshObjLoader name="loader" filename="tube.obj"
<MeshOBJLoader name="loader" filename="tube.obj"
scale3d="0.01 0.01 0.01" translation="0 0.0206 0" />
<TriangleSetTopologyContainer name="topo" src="@loader" />
<MechanicalObject name="TubeMO" />
</Node>

<Node name="Tube">
<EulerImplicit />
<SparseLDLSolver/>
<EulerImplicitSolver />
<SparseLDLSolver template="CompressedRowSparseMatrixMat3x3d"/>

<TriangleSetTopologyContainer name="topo" src="@/TubeMesh/topo" />

<MechanicalObject template="Vec3d" />

<FixedConstraint indices="0-63" />
<FixedProjectiveConstraint indices="0-63" />

<LinearSolverConstraintCorrection />

<UniformMass mass="1"/>
<UniformMass totalMass="1"/>

<Node name="Collision">
<TriangleSetTopologyContainer name="topo" src="@../topo" />
Expand All @@ -77,23 +107,23 @@
<IdentityMapping input="@.." output="@."/>

<!--<Point name="tube_collis_point" group="10" />-->
<Line name="tube_collis_line" group="10"/>
<LineCollisionModel name="tube_collis_line" group="10"/>
<!--<Triangle name="tube_collis_line" bothSide="true" group="10"/>-->
</Node>

</Node>

<Node name="Cube">
<EulerImplicit />
<SparseLDLSolver/>
<EulerImplicitSolver />
<SparseLDLSolver template="CompressedRowSparseMatrixMat3x3d"/>


<Mesh src="@/VolMesh/loader" />
<MeshTopology src="@/VolMesh/loader" />
<MechanicalObject name="MO" src="@/VolMesh/loader"/>
<BoxROI name="top" box="-0.0076 0.0149 -0.0076 0.0076 0.0178 0.0076" drawBoxes="true" />
<BoxROI name="bottom" box="-0.0076 -0.0001 -0.0076 0.0076 0.0001 0.0076" drawBoxes="true" />-->
<BoxROI name="bottom" box="-0.0076 -0.0001 -0.0076 0.0076 0.0001 0.0076" drawBoxes="true" />

<UniformMass mass="0.001"/>
<UniformMass totalMass="0.001"/>

<VTKExporter filename="result_aspiration.vtk" XMLformat="false" listening="true"
edges="0" triangles="0" quads="0" tetras="1"
Expand All @@ -115,15 +145,15 @@
/>
</Node>

<!--<FixedConstraint indices="@bottom.indices" />-->
<!--<FixedProjectiveConstraint indices="@bottom.indices" />-->

<LinearSolverConstraintCorrection/>

<Node name="CubeCollision">
<Mesh src="@/SurfMesh/topo" />
<MeshTopology src="@/SurfMesh/topo" />
<MechanicalObject />
<!--<Point name="cube_collis_point" group="11" />-->
<Line name="cube_collis_line" group="11" />
<LineCollisionModel name="cube_collis_line" group="11" />
<!--<Triangle name="cube_collis_triangle" computeNormals="false" bothSide="true" group="11" />-->
<BarycentricMapping input="@.." output="@." />

Expand All @@ -136,16 +166,16 @@
</Node>

<Node name="Cube-composite">
<EulerImplicit />
<SparseLDLSolver/>
<EulerImplicitSolver />
<SparseLDLSolver template="CompressedRowSparseMatrixMat3x3d"/>


<Mesh src="@/VolMesh/loader" />
<MeshTopology src="@/VolMesh/loader" />
<MechanicalObject name="MO" src="@/VolMesh/loader"/>
<BoxROI name="top" box="-0.0076 0.0149 -0.0076 0.0076 0.0178 0.0076" drawBoxes="true" />
<BoxROI name="bottom" box="-0.0076 -0.0001 -0.0076 0.0076 0.0001 0.0076" drawBoxes="true" />-->

<UniformMass mass="0.001"/>
<UniformMass totalMass="0.001"/>

<VTKExporter filename="result_aspiration2.vtk" XMLformat="false" listening="true"
edges="0" triangles="0" quads="0" tetras="1"
Expand All @@ -168,15 +198,15 @@
/>
</Node>

<!--<FixedConstraint indices="@bottom.indices" />-->
<!--<FixedProjectiveConstraint indices="@bottom.indices" />-->

<LinearSolverConstraintCorrection/>

<Node name="CubeCollision">
<Mesh src="@/SurfMesh/topo" />
<MeshTopology src="@/SurfMesh/topo" />
<MechanicalObject />
<!--<Point name="cube_collis_point" group="11" />-->
<Line name="cube_collis_line" group="11" />
<LineCollisionModel name="cube_collis_line" group="11" />
<!--<Triangle name="cube_collis_triangle" computeNormals="false" bothSide="true" group="11" />-->
<BarycentricMapping input="@.." output="@." />

Expand All @@ -189,7 +219,7 @@
</Node>

<!--<Node name="TubeRender">-->
<!--<MeshObjLoader name="loader" filename="tube.obj"-->
<!--<MeshOBJLoader name="loader" filename="tube.obj"-->
<!--scale3d="0.01 0.01 0.01" translation="0 0.0205 0" />-->
<!--<TriangleSetTopologyContainer name="topo" src="@loader" />-->
<!--<MechanicalObject name="TubeMO" />-->
Expand Down
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