From a84180081a98a9619155e7ff0bb31ee7d93cb434 Mon Sep 17 00:00:00 2001
From: epernod <erik.pernod@gmail.com>
Date: Mon, 5 Oct 2026 09:58:08 +0200
Subject: [PATCH 1/4] [scenes] Update scenes to be compatible with changes in
 SOFa regarding IntegrationScheme

---
 scenes/beamContact.scn | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scenes/beamContact.scn b/scenes/beamContact.scn
index 33a7e0d..4f35b69 100644
--- a/scenes/beamContact.scn
+++ b/scenes/beamContact.scn
@@ -46,7 +46,7 @@
         </Node>
 
 <!--        <Node name="Needle">
-                <EulerImplicitSolver rayleighMass="0" rayleighStiffness="0" />
+                <EulerImplicitIntegrationScheme rayleighMass="0" rayleighStiffness="0" />
                 <SparseLUSolver />
 
                 <EdgeSetTopologyContainer name="Container" position="0 0 0   2 0 0    4 0 0    6 0 0    8 0 0   10 0 0   12 0 0    14 0 0   16 0 0" edges="0 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8"/>
@@ -74,7 +74,7 @@
         </Node>-->
 
         <Node name="Needle">
-               <EulerImplicitSolver rayleighMass="0" rayleighStiffness="0" />
+               <EulerImplicitIntegrationScheme rayleighMass="0" rayleighStiffness="0" />
                <SparseLUSolver />
 
                 <MechanicalObject name="ms" template="Rigid" dy="20" />
@@ -117,7 +117,7 @@
         </Node>-->
 
         <Node name="GEL">
-                <EulerImplicitSolver rayleighMass="0.1" rayleighStiffness="0.1" />
+                <EulerImplicitIntegrationScheme rayleighMass="0.1" rayleighStiffness="0.1" />
                 <SparseLDLSolver name="precond" />
 
                 <TetrahedronSetTopologyContainer name="Container" src="@../Topology/GelVolume/Container" />

From 9e9de9cc013f75e2c103672c114a49ffb1188fce Mon Sep 17 00:00:00 2001
From: erik pernod <erik.pernod@gmail.com>
Date: Mon, 5 Oct 2026 11:55:18 +0200
Subject: [PATCH 2/4] Delete scenes/beamContact.scn

---
 scenes/beamContact.scn | 173 -----------------------------------------
 1 file changed, 173 deletions(-)
 delete mode 100644 scenes/beamContact.scn

diff --git a/scenes/beamContact.scn b/scenes/beamContact.scn
deleted file mode 100644
index 4f35b69..0000000
--- a/scenes/beamContact.scn
+++ /dev/null
@@ -1,173 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<Node name="root" dt="0.01" gravity="0 0 0" >
-        <RequiredPlugin pluginName="ConstraintGeometryPlugin" />
-        <RequiredPlugin pluginName="CollisionAlgorithmPlugin" />
-	<RequiredPlugin pluginName="GeomagicDriverPlugin" />
-
-        <VisualStyle displayFlags="showVisualModels hideBehaviorModels showCollisionModels hideMappings hideForceFields hideWireframe showForceFields" />
-
-        <FreeMotionAnimationLoop />
-        <GenericConstraintSolver maxIt="100" tolerance="0.000000001" printLog="false" />
-
-        <Node name="Topology" >
-                    <Node name="GelVolume" >
-<!--                            <SparseGrid name="HexaTop" cellWidth="1.2" fileTopology="mesh/Armadillo_simplified.obj" />-->
-                            <RegularGrid name="HexaTop" n="8 8 8	" min="-10 -6 -10" max="10 14 10" />
-<!--                            <RegularGrid name="HexaTop" n="2 2 2" min="-10 -6 -10" max="10 14 10" /> -->
-
-                            <TetrahedronSetTopologyContainer name="Container" position="@HexaTop.position" />
-                            <TetrahedronSetTopologyModifier name="Modifier"/>
-                            <Hexa2TetraTopologicalMapping input="@HexaTop" output="@Container" swapping="false" />
-                    </Node>
-
-                    <Node name="GelSurface" >
-<!--                            <Mesh   name="Container" cellWidth="2.0" filename="mesh/Armadillo_simplified.obj" />-->
-
-                            <TriangleSetTopologyContainer name="Container" position="@../GelVolume/HexaTop.position" />
-                            <TriangleSetTopologyModifier name="Modifier"/>
-                            <Tetra2TriangleTopologicalMapping input="@../GelVolume/Container" output="@Container" flipNormals="true"/>
-
-<!--                            <CubeTopology name="cubeTop" nx="20" ny="5" nz="5" min="@../GelVolume/HexaTop.min" max="@../GelVolume/HexaTop.max" />-->
-<!--                            <TriangleSetTopologyContainer name="Container" position="@cubeTop.position" />-->
-<!--                            <TriangleSetTopologyModifier name="Modifier"/>-->
-<!--                            <Quad2TriangleTopologicalMapping input="@cubeTop" output="@Container" />-->
-                    </Node>
-        </Node>
-
-        <Node name="OmniControler">
-                <GeomagicDriver name="omni" tags="sensable" scale="3" omniVisu="0" positionBase="0 0 0" orientationBase="0 1 0 0" orientationTool="0 0.707107 0 0.707107"/>
-                <MechanicalObject name="ms" template="Rigid" position="@omni.posDevice" free_position="@omni.posDevice" showObject="true" showObjectScale="0" />
-<!--                <MechanicalObject name="ms" template="Rigid" position="-20 0 -8  0 0 0 1" showObject="true" showObjectScale="0" />-->
-<!--                <MechanicalObject name="ms" template="Rigid" position="-50 -30 -50  0 0 0 1" showObject="true" showObjectScale="0" />-->
-<!--                <MechanicalObject name="ms" template="Rigid" position="0.55 22 -12.6 0 1" showObject="true" showObjectScale="0" />-->
-
-<!--                 <WriteState filename="posNeedle" /> -->
-<!--                <ReadState filename="posNeedle" />-->
-        </Node>
-
-<!--        <Node name="Needle">
-                <EulerImplicitIntegrationScheme rayleighMass="0" rayleighStiffness="0" />
-                <SparseLUSolver />
-
-                <EdgeSetTopologyContainer name="Container" position="0 0 0   2 0 0    4 0 0    6 0 0    8 0 0   10 0 0   12 0 0    14 0 0   16 0 0" edges="0 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8"/>
-
-                <MechanicalObject name="ms" template="Rigid" />
-                <BeamFEMForceField name="FEM" radius="0.8" youngModulus="1e7" poissonRatio="0.45"/>
-                <RestShapeSpringsForceField external_rest_shape="@../OmniControler/ms" stiffness="5000"  angularStiffness="500000" points="0" external_points="0" />
-                
-
-                <Node name="Collision">
-                        <EdgeSetTopologyContainer name="Container" src="@../Container" />
-                        <MechanicalObject name="ms" />
-
-                        <EdgeGeometry name="needle" />
-                        <Sphere radius="0.1" />
-                        <BeamLinearMapping localCoord="false" />
-                </Node>
-
-                <Node name="Base">
-                        <MechanicalObject name="ms" template="Rigid" position="0 0 0  0 0 0 1"   />
-                        <RigidRigidMapping />
-                </Node>
-
-                <LinearSolverConstraintCorrection />
-        </Node>-->
-
-        <Node name="Needle">
-               <EulerImplicitIntegrationScheme rayleighMass="0" rayleighStiffness="0" />
-               <SparseLUSolver />
-
-                <MechanicalObject name="ms" template="Rigid" dy="20" />
-                <RestShapeSpringsForceField external_rest_shape="@../OmniControler/ms" stiffness="500000"  angularStiffness="500000" points="0" external_points="0" />
-
-                <Node name="Collision">
-<!--                       <EdgeSetTopologyContainer name="Container" position="0 0 0   2 0 0    4 0 0    6 0 0    8 0 0   10 0 0   12 0 0    14 0 0   16 0 0" edges="0 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8"/>-->
-                         <EdgeSetTopologyContainer name="Container" position="0 0 0   16 0 0" edges="0 1 "/>
-<!--                          <EdgeSetTopologyContainer name="Container" position="0 0 0 " />-->
-			<MechanicalObject name="ms" />
-
-                        <PointGeometry name="point" />
-<!--                        <EdgeGeometry name="needle" />-->
-                        
-			<RigidMapping />
-                </Node>
-                
-                <Node name="Base">
-                        <MechanicalObject name="ms" template="Rigid" position="0 0 0  0 0 0 1"   />
-                        <RigidRigidMapping />
-                </Node>
-
-                <LinearSolverConstraintCorrection />
-        </Node>
-
-<!--        <Node name="ForceFeedback" >
-                <MechanicalObject name="ms" template="Rigid" showObject="true" src="@../Needle/Base/ms" />
-
-                <Node name="Collision">
-                        <EdgeSetTopologyContainer name="Container" src="@../../Needle/Collision/Container" />
-                        <MechanicalObject name="ms" constraint="@../../Needle/Collision/ms.constraint" />
-
-                        <Line color="1 0 0 1" />
-                        <Point color="1 0 0 1"  />
-
-                        <RigidMapping />
-                </Node>
-
-                <LCPForceFeedback tags="sensable"  activate="true" printLog="false" forceCoef="0.05" solverTimeout="0.0001" />
-        </Node>-->
-
-        <Node name="GEL">
-                <EulerImplicitIntegrationScheme rayleighMass="0.1" rayleighStiffness="0.1" />
-                <SparseLDLSolver name="precond" />
-
-                <TetrahedronSetTopologyContainer name="Container" src="@../Topology/GelVolume/Container" />
-
-                <MechanicalObject name="ms" />
-                <UniformMass totalmass="1" />
-
-                <TetrahedronFEMForceField youngModulus="1000" poissonRatio="0.45" />
-                <BoxROI name="box" box="-10 -6 -10 10 -4 10" drawBoxes="true" />
-<!--                 <RestShapeSpringsForceField external_rest_shape="@./ms" points="@box.indices" stiffness="500" angularStiffness="500"  /> -->
-                <FixedConstraint indices="@box.indices"  />
-
-                <Node name="Surface">
-			<TriangleSetTopologyContainer name="Container" src="@../../Topology/GelSurface/Container"/>
-<!--                         <TriangleSetTopologyContainer name="Container" triangles="0 1 2" position="-10 -6 0    10 -6 0    -10 -6 10"/> -->
-                        <MechanicalObject name="ms" />
-
-<!--                        <BezierTriangleGeometry name="surface" />-->
-<!--                         <TriangleGeometry name="surface" phong="false" /> -->
-<!--                        <EdgeLinearInterpolation name="surface" />-->
-
-                        <TriangleGeometry name="surface" />
-<!--			<AABBGeometry name="AABB" geometry="surface" />-->
-			
-			<BarycentricMapping />
-                </Node>
-
-<!--                <Node name="Trajectory">
-                        <EdgeSetTopologyContainer name="Container" />
-                        <EdgeSetTopologyModifier name="Modifier" />
-                        <MechanicalObject name="ms" />
-                        <NeedleTrajectoryGeometry name="trajectory" entryDist="1" constraintDist="2" clearTrajectory="false" />
-                        <BarycentricMapping listening="true" useRestPosition="false" />
-                </Node>-->
-                
-                <LinearSolverConstraintCorrection solverName="precond"/>
-	</Node>	
-
-<!--        <BilateralResponse name="uni"/>-->
-        <UnilateralResponse name="uni" />
-        <CollisionDetectionAlgorithm name="contactAlgo" />
-
-
-        <ConstraintPair response="uni" algo="contactAlgo" from="Needle/Collision/point" dest="GEL/Surface/surface" />
-
-
-<!--	<CollisionDetectionAlgorithm name="contactAlgo2" from="Needle/Collision/needle" dest="GEL/Surface/surface" />-->
-	
-
-
-<!--        <Constraint algorithm="contactAlgo" />-->
-<!--	<UnilateralContactConstraint algorithm="contactAlgo" />-->
-</Node>

From 8a43eab71573a4bca14352b166b4045690bf5ca6 Mon Sep 17 00:00:00 2001
From: Themis Skamagkis <themisskamagkis@gmail.com>
Date: Mon, 5 Oct 2026 12:05:47 +0200
Subject: [PATCH 3/4] remove peripheral files

---
 scenes/beamContact.scn.log            | 9 ---------
 scenes/beamContact.scn.qglviewer.view | 2 --
 2 files changed, 11 deletions(-)
 delete mode 100644 scenes/beamContact.scn.log
 delete mode 100644 scenes/beamContact.scn.qglviewer.view

diff --git a/scenes/beamContact.scn.log b/scenes/beamContact.scn.log
deleted file mode 100644
index 30a2b2e..0000000
--- a/scenes/beamContact.scn.log
+++ /dev/null
@@ -1,9 +0,0 @@
-
---- NEW SESSION: 05/03/2018 16:59:15 ---
-/genericConstraintSolver1.printLog = 1
-
---- NEW SESSION: 05/03/2018 17:11:48 ---
-/genericConstraintSolver1.printLog = 1
-
---- NEW SESSION: 05/03/2018 18:26:42 ---
-/genericConstraintSolver1.printLog = 1
diff --git a/scenes/beamContact.scn.qglviewer.view b/scenes/beamContact.scn.qglviewer.view
deleted file mode 100644
index f374103..0000000
--- a/scenes/beamContact.scn.qglviewer.view
+++ /dev/null
@@ -1,2 +0,0 @@
--8.59703 27.6607 -160.361
-0.00394153 0.996749 0.08005 -0.00821903

From 613061c594abc33c15fcdacab75813916809e338 Mon Sep 17 00:00:00 2001
From: Themis Skamagkis <themisskamagkis@gmail.com>
Date: Mon, 5 Oct 2026 12:06:58 +0200
Subject: [PATCH 4/4] Remove liver scene. Old and not demonstrating anything of
 consequence

---
 scenes/liver.scn | 67 ------------------------------------------------
 1 file changed, 67 deletions(-)
 delete mode 100644 scenes/liver.scn

diff --git a/scenes/liver.scn b/scenes/liver.scn
deleted file mode 100644
index ba4ab1e..0000000
--- a/scenes/liver.scn
+++ /dev/null
@@ -1,67 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<Node name="Root" gravity="0 -15 0" dt="0.05">
-        <RequiredPlugin pluginName="CollisionAlgorithm"/>
-        <RequiredPlugin pluginName="ConstraintGeometry"/>
-		
-        <VisualStyle displayFlags="showVisualModels hideBehaviorModels showCollisionModels hideMappings hideForceFields showWireframe showInteractionForceFields" />
-        <FreeMotionAnimationLoop name="CollisionAnimationLoop"/>
-        <GenericConstraintSolver maxIterations="200" tolerance="0.0001" />
-
-        <CollisionLoop />
-
-        <FindClosestProximityAlgorithm name="algo" from="@Liver/Collision/Geometry" dest="@Plane/Geometry" />
-        <DistanceFilter name="distance" algo="@algo" distance="0.1" />
-    
-        
-        <Node name="Liver">
-                <EulerImplicit name="EulerImplicit" rayleighMass="0.1" rayleighStiffness="0.1" />
-                <SparseLDLSolver template="CompressedRowSparseMatrixMat3x3d" />
-
-                <MeshGmshLoader name="loader" filename="mesh/liver.msh"/>
-                <MeshTopology name="Topology" tetrahedra="@loader.tetrahedra" />
-                <MechanicalObject name="State3D" position="@loader.position" rest_position="@loader.position"/>
-
-                <TetrahedronFEMForceField name="TetrahedronFEMForceField" poissonRatio="0.4" youngModulus="50" />
-
-                <UniformMass name="UniformMass" totalMass="1"/>
-
-                <Node name="Collision">
-                        <TriangleSetTopologyContainer name="Container" position="@../loader.position"   />
-                        <TriangleSetTopologyModifier name="Modifier"/>
-                        <Tetra2TriangleTopologicalMapping input="@../Topology" output="@Container" flipNormals="false"/>
-                        <MechanicalObject name="state" />
-
-                        <TriangleGeometry name="Geometry" color="0 1 0 1" />
-                        <AABBBroadPhase name="AABB" geometry="@Geometry" nbox="8 8 8" />
-						<PhongTriangleNormalHandler name="handler" geometry="@Geometry" />
-						
-                        <BarycentricMapping name="BarycentricMapping"/>
-                </Node>
-
-                <Node name="Surface">
-                        <MeshObjLoader name="loader" filename="mesh/liver-smooth.obj"/>
-                        <MeshTopology name="Topology1" triangles="@loader.triangles" />
-                        <OglModel name="OglModel" color="0 1 0"  src='@loader'/>
-                        <BarycentricMapping name="BarycentricMapping"/>
-                </Node>
-
-                <LinearSolverConstraintCorrection />
-        </Node>
-
-        <Node name="Plane">
-                <MeshObjLoader name="loader" filename="mesh/box_inside.obj"/>
-                <MeshTopology name="Topology1" triangles="@loader.triangles" />
-                <MechanicalObject name="State3D1" dy="1" position="@loader.position" />
-                <OglModel name="OglModel" color="1 1 1 0.8"/>
-                <TriangleGeometry name="Geometry" color="1 1 1 0.6" />
-				<GouraudTriangleNormalHandler name="handler" geometry="@Geometry" />
-				
-<!--                 <AABBBroadPhase name="AABB" geometry="@Geometry" nbox="8 8 8" color="1 0 0 0.3" /> -->
-        </Node>
-        
-        <ContactDirection name="second" handler="@Plane/handler"/>
-<!-- 		<FirstDirection name="second" handler="@Liver/Collision/handler"/> -->
-<!-- 		<SecondDirection name="second" handler="@Plane/handler"/> -->
-        <ConstraintUnilateral name="constraint" input="@algo.output" mu="0" directions="@second" />
-
-</Node>