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FillReducingOrdering

Reorder the degrees of freedom to reduce fill-in

Vec3d

Templates:

  • Vec3d

Target: SofaMatrix

namespace: sofa::component::linearsolver

parents:

  • DataEngine

Data

Name Description Default value
name object name unnamed
printLog if true, emits extra messages at runtime. 0
tags list of the subsets the object belongs to
bbox this object bounding box
componentState The state of the component among (Dirty, Valid, Undefined, Loading, Invalid). Undefined
listening if true, handle the events, otherwise ignore the events 0
orderingMethod Ordering method. nestedDissection is the multilevel nested dissection algorithm implemented in the METIS library. approximateMinimumDegree is the approximate minimum degree algorithm implemented in the Eigen library. nestedDissection
Outputs
permutation Output vector of indices mapping the reordered vertices to the initial list
invPermutation Output vector of indices mapping the initial vertices to the reordered list
position Reordered position vector
hexahedra Reordered hexahedra
tetrahedra Reordered tetrahedra
Name Description Destination type name
context Graph Node containing this object (or BaseContext::getDefault() if no graph is used) BaseContext
slaves Sub-objects used internally by this object BaseObject
master nullptr for regular objects, or master object for which this object is one sub-objects BaseObject
mstate Mechanical state to reorder MechanicalState<Vec3d>
topology Topology to reorder BaseMeshTopology

Examples

FillReducingOrdering.scn

<!--
This scene introduces the usage of the component FillReducingOrdering.
See its class description for more details.

The scene compares two simulations in which only the vertices order differs:
- The Node "NoReorder" simulates the initial mesh.
- The Node "Reorder" simulates the reordered mesh.
-->
<Node name="root" gravity="-1.8 0 100" dt="0.001">
    <RequiredPlugin name="Sofa.Component.Constraint.Projective"/> <!-- Needed to use components [FixedProjectiveConstraint] -->
    <RequiredPlugin name="Sofa.Component.Engine.Transform"/> <!-- Needed to use components [MapIndices TransformEngine] -->
    <RequiredPlugin name="Sofa.Component.IO.Mesh"/> <!-- Needed to use components [MeshGmshLoader] -->
    <RequiredPlugin name="Sofa.Component.LinearSolver.Direct"/> <!-- Needed to use components [EigenSparseLU] -->
    <RequiredPlugin name="Sofa.Component.Mass"/> <!-- Needed to use components [MeshMatrixMass] -->
    <RequiredPlugin name="Sofa.Component.ODESolver.Backward"/> <!-- Needed to use components [EulerImplicitSolver] -->
    <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 [TetrahedronSetGeometryAlgorithms TetrahedronSetTopologyContainer] -->
    <RequiredPlugin name="Sofa.Component.Visual"/> <!-- Needed to use components [VisualStyle] -->
    <RequiredPlugin name="Sofa.GL.Component.Rendering2D"/> <!-- Needed to use components [OglLabel] -->
    <RequiredPlugin name="SofaMatrix"/> <!-- Needed to use components [FillReducingOrdering GlobalSystemMatrixImage] -->

    <VisualStyle displayFlags="showForceFields hideVisualModels showBehaviorModels" />

    <Node name="Mesh">

        <MeshGmshLoader name="loader" filename="mesh/truthcylinder1.msh" />
        <TetrahedronSetTopologyContainer src="@loader" name="topologyContainer"/>
        <MechanicalObject name="dofs" src="@loader"/>

    </Node>

    <Node name="NoReorder" activated="true">
        <EulerImplicitSolver name="odeImplicitSolver" />
        <MatrixLinearSystem name="system"/>
        <EigenSparseLU name="solver" template="CompressedRowSparseMatrixd"/>

        <GlobalSystemMatrixImage linearSystem="@system"/>

        <TetrahedronSetTopologyContainer src="@../Mesh/loader" name="topologyContainer"/>
        <MechanicalObject name="dofs" src="@../Mesh/loader"/>
        <MeshMatrixMass totalMass="15" topology="@topologyContainer"/>

        <FixedProjectiveConstraint name="fix" indices="0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 268 269 270 271 343 345" />
        <TetrahedronFEMForceField name="FEM" youngModulus="1000" poissonRatio="0.49" method="large" />

    </Node>

    <Node name="Reorder" activated="true">
        <EulerImplicitSolver name="odeImplicitSolver" />
        <MatrixLinearSystem name="system"/>
        <EigenSparseLU name="solver" template="CompressedRowSparseMatrixd"/>

        <GlobalSystemMatrixImage linearSystem="@system"/>

        <FillReducingOrdering name="reorder" mstate="@../Mesh/dofs" topology="@../Mesh/topologyContainer" orderingMethod="AMD"/>
        <TransformEngine name="transform" input_position="@reorder.position" translation="10 0 0"/>

        <TetrahedronSetTopologyContainer name="topologyContainer" tetrahedra="@reorder.tetrahedra" position="@transform.output_position"/>
        <TetrahedronSetGeometryAlgorithms name="geomAlgo"/>

        <MechanicalObject name="dofs" position="@transform.output_position"/>
        <MeshMatrixMass totalMass="15" topology="@topologyContainer"/>

        <MapIndices name="perm" template="int" in="@../NoReorder/fix.indices" indices="@reorder.permutation"/>
        <FixedProjectiveConstraint indices="@perm.out" />
        <TetrahedronFEMForceField name="FEM" youngModulus="1000" poissonRatio="0.49" method="large" />

    </Node>

    <OglLabel label="Nb non-zeroes:" fontsize="30"/>
    <OglLabel prefix="  Without reordering: " label="@NoReorder/solver.L_nnz" fontsize="20" y="70"/>
    <OglLabel prefix="  With reordering: " label="@Reorder/solver.L_nnz" fontsize="20" y="120"/>
</Node>

def createScene(root_node):

   root = root_node.addChild('root', gravity="-1.8 0 100", dt="0.001")

   root.addObject('RequiredPlugin', name="Sofa.Component.Constraint.Projective")
   root.addObject('RequiredPlugin', name="Sofa.Component.Engine.Transform")
   root.addObject('RequiredPlugin', name="Sofa.Component.IO.Mesh")
   root.addObject('RequiredPlugin', name="Sofa.Component.LinearSolver.Direct")
   root.addObject('RequiredPlugin', name="Sofa.Component.Mass")
   root.addObject('RequiredPlugin', name="Sofa.Component.ODESolver.Backward")
   root.addObject('RequiredPlugin', name="Sofa.Component.SolidMechanics.FEM.Elastic")
   root.addObject('RequiredPlugin', name="Sofa.Component.StateContainer")
   root.addObject('RequiredPlugin', name="Sofa.Component.Topology.Container.Dynamic")
   root.addObject('RequiredPlugin', name="Sofa.Component.Visual")
   root.addObject('RequiredPlugin', name="Sofa.GL.Component.Rendering2D")
   root.addObject('RequiredPlugin', name="SofaMatrix")
   root.addObject('VisualStyle', displayFlags="showForceFields hideVisualModels showBehaviorModels")

   mesh = root.addChild('Mesh')

   mesh.addObject('MeshGmshLoader', name="loader", filename="mesh/truthcylinder1.msh")
   mesh.addObject('TetrahedronSetTopologyContainer', src="@loader", name="topologyContainer")
   mesh.addObject('MechanicalObject', name="dofs", src="@loader")

   no_reorder = root.addChild('NoReorder', activated="true")

   no_reorder.addObject('EulerImplicitSolver', name="odeImplicitSolver")
   no_reorder.addObject('MatrixLinearSystem', name="system")
   no_reorder.addObject('EigenSparseLU', name="solver", template="CompressedRowSparseMatrixd")
   no_reorder.addObject('GlobalSystemMatrixImage', linearSystem="@system")
   no_reorder.addObject('TetrahedronSetTopologyContainer', src="@../Mesh/loader", name="topologyContainer")
   no_reorder.addObject('MechanicalObject', name="dofs", src="@../Mesh/loader")
   no_reorder.addObject('MeshMatrixMass', totalMass="15", topology="@topologyContainer")
   no_reorder.addObject('FixedProjectiveConstraint', name="fix", indices="0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 268 269 270 271 343 345")
   no_reorder.addObject('TetrahedronFEMForceField', name="FEM", youngModulus="1000", poissonRatio="0.49", method="large")

   reorder = root.addChild('Reorder', activated="true")

   reorder.addObject('EulerImplicitSolver', name="odeImplicitSolver")
   reorder.addObject('MatrixLinearSystem', name="system")
   reorder.addObject('EigenSparseLU', name="solver", template="CompressedRowSparseMatrixd")
   reorder.addObject('GlobalSystemMatrixImage', linearSystem="@system")
   reorder.addObject('FillReducingOrdering', name="reorder", mstate="@../Mesh/dofs", topology="@../Mesh/topologyContainer", orderingMethod="AMD")
   reorder.addObject('TransformEngine', name="transform", input_position="@reorder.position", translation="10 0 0")
   reorder.addObject('TetrahedronSetTopologyContainer', name="topologyContainer", tetrahedra="@reorder.tetrahedra", position="@transform.output_position")
   reorder.addObject('TetrahedronSetGeometryAlgorithms', name="geomAlgo")
   reorder.addObject('MechanicalObject', name="dofs", position="@transform.output_position")
   reorder.addObject('MeshMatrixMass', totalMass="15", topology="@topologyContainer")
   reorder.addObject('MapIndices', name="perm", template="int", in="@../NoReorder/fix.indices", indices="@reorder.permutation")
   reorder.addObject('FixedProjectiveConstraint', indices="@perm.out")
   reorder.addObject('TetrahedronFEMForceField', name="FEM", youngModulus="1000", poissonRatio="0.49", method="large")

   root.addObject('OglLabel', label="Nb non-zeroes:", fontsize="30")
   root.addObject('OglLabel', prefix="  Without reordering: ", label="@NoReorder/solver.L_nnz", fontsize="20", y="70")
   root.addObject('OglLabel', prefix="  With reordering: ", label="@Reorder/solver.L_nnz", fontsize="20", y="120")