[Hugo]

Hi @simon !

Looking at your scene, it seems you are more looking for boundary conditions (fixing your 3D beam) or a constraint than for a mapping.
Right?
Do you want a part of your deformable to be rigidly attached to a rigid frame?

Did you take a look at the following examples?

• examples/Components/constraint/BilateralInteractionConstraint.scn
• examples/Components/constraint/FixedConstraint.scn
• examples/Components/constraint/AttachConstraint.scn

Best

Hugo

[Hugo]

Hey @outtt

You’re correct. I will add this to my todolist.

Adding a MeshMatrixMass in a python scene would look like:

node.createObject("MeshMatrixMass", name="SparseMass", massDensity="0.1", topology="@TopologyContainerLink")

I hope this helps.
Best

Hugo

[Hugo]

Thanks for sharing your updated solution @zacharyjay !
I close the topic.

Hugo

[Hugo]

Hey @zacharyjay

Sorry your post slipped through our reviews. My apologies.

I am sorry this IdMap error does not ring a bell.. I’ll ask around me.
Are these the only 2 compilation errors you get?
Have you given a try to the latest SOFA release v19.12 ?

Best,

Hugo

[Hugo]

hey @balazs

Welcome on the SOFA forum!
Machine learning trained with simulations, how trendy is it! Interesting topic!

A plugin already exists allowing to use SOFA and interact with the simulation within a Python3 environment: SOFAPython3 plugin. In a python script, you can design, run and interact with a simulation and its parameters (and much more!).

Is this what you are looking for?
What do you mean exactly by “access the rendered simulation view from within Python3”?

Best wishes,

Hugo

[Hugo]

Hey @fleonard

I am sorry for this late reply.
That’s an interesting and challenging objective. I am no expert of the collision detection pipeline however.

Could you share your code on any GitHub repo ?
I will discuss with experts next week and get back to you.

Best

Hugo

[Hugo]

Hi @joshuaf

I am really sorry for this delayed reply.
I wanted to find some time to look at your simulation.

Your simulation includes constraints, solved following the Lagrange multiplier method. You are right, the force that must be applied to compensate the gravity must be scaled by 0.01. It actually corresponds to the time step.

I think this comes from the Lagrange constraint resolution which involves the time step. I need to get through the equations to provide you a complete explanation. I will get back to you next week.

Sorry again for our latency!
Best wishes,

Hugo

[Hugo]

Hi @marina

Good to see you on the forum!
Yes creating subpart of an object with different representations (e.g. different collision models) should be possible using the SubsetMapping. You can have a look at the example: examples/Components/mapping/SubsetMapping.scn

I hope this helps.
Best,

Hugo

[Hugo]

Hi @bence,

It must be stressed that Beamadapter is a private plugin.
You won’t really get the support from the community.

Could you please contact me in PM and enclose your scene file+meshes please?

Best

Hugo

[Hugo]

Hi @lakehanne

Usually C++ controllers tend to disappear with the growth of the Python scripting. This is due to the fact that Python allows for an easy, live scripting providing a maximum freedom to the user. On the other hand, C++ requires C++ coding, compilation and a controller usually implements one “controlling” feature.

If you implemented your own ForceField, it should work fine with SofaPython, since the forcefield class has already been bound.

For controller examples in C++, you can take a look at MechanicalStateController (in modules/SofaUserInteraction). There, you could implement the function handleEvent() (handling the respective events: onBeginAnimationStep and onEndAnimationStep).

Best,

Hugo

[Hugo]

Great. Shall we close this topic then?

Hugo

[Hugo]

Hi @lakehanne

I’m glad if it helped. Can we close the topic?
Anyway, keep us posted from your progress (papers, video, pull-requests etc.)!

Best,

Hugo

[Hugo]

Dear @lakehanne

Yes the new SOFAPython plugin (using Python3 instead of Python2) allows such an implementation, you can see an example for a forcefield here.

You might have to rewrite the entire scene. We had a script translating a *.scn into a *.py (see scn2python.py script) but this was compatible for Python2.

Best,

Hugo

[Hugo]

Dear @lakehanne

Your variable dr_pos_vecs will contain the field ‘position’ of your Vec3 MechanicalObject. It will therefore be a vector with a size corresponding to the number of nodes in your mesh, with 3 reals (x,y,z) for each node.
How many points does your mesh include?
What is the size returned by the MechanicalObject position vector?

Best wishes,

Hugo

PS: short question, why not using Python to script interactive features in your simulation?

[Hugo]

Hi @joshuaf

Sorry for keeping you waiting.
I think the pull request #1245 will fix your problem. Do not hesitate to give it a try by cherry-picking it.

Best wishes,

Hugo

[Hugo]

Hi @nguyenvanpho

Sorry for the delayed reply.
The link seems to be dead. Could you upload it again please? Could you also let us know which version of SOFA are you using?

Best

Hugo

[Hugo]

Dear @outtt

This is a complex question.
First of all, in FEM, tetrahedra are known to be prone to “distortion” or more commonly called “numerical locking”. Their efficiency in term of integration has this drawback. Hexahedra are more robust to this problem.

But looking into your scene, the first point would be to use a dense mass (MeshMatrixMass) and not a lumped mass (DiagonalMass). Second, you need to use appropriate values for your physical properties (mass density, Young’s modulus etc). Finally, when this is not sufficient, decreasing the mesh refinement and the time step is the only solution.

I hope I gave several point of investigation here. Do not hesitate to keep us posted.
Best wishes,

Hugo

PS: curious question, why are you not using boundary conditions (like using the FixedConstraint) and applying a RestShapeSpringsForceField instead ?

[Hugo]

Hi @jieying

Sorry for the late reply!
I tested your scene multithreading.scn it seems to run.
Here is the simulation:

and no error is given.

Do you still have the error?
Could you copy paste the console output?
Could you tell us your SOFA versions?

Below the scene slightly modified:

<?xml version="1.0"?>
<Node name="root" gravity="0 -50 0" dt="0.001">    
    <RequiredPlugin pluginName="MultiThreading" />
    <AnimationLoopParallelScheduler name="mainLoop" threadNumber="0" />
        

    <VisualStyle displayFlags="hideBehaviorModels hideVisualModels showCollisionModels showInteractionForcefields" />
    <FreeMotionAnimationLoop solveVelocityConstraintFirst="0"/>
    <LCPConstraintSolver maxIt="1000" tolerance="1e-6" mu="0.9"/>
    <DefaultPipeline depth="5" verbose="0" draw="0" />
    <BruteForceDetection name="N2" />
    <MinProximityIntersection alarmDistance="0.03" contactDistance="0.02" />
    <DiscreteIntersection/>
    <DefaultContactManager name="Response" response="FrictionContact"/>

    <Node name="FloorScene">

<!--         <VisualStyle displayFlags="showBehaviorModels" />
        <FreeMotionAnimationLoop solveVelocityConstraintFirst="0"/>
        <LCPConstraintSolver maxIt="1000" tolerance="1e-6" mu="0.9"/>
        <DefaultPipeline depth="5" verbose="0" draw="0" />
        <BruteForceDetection name="N2" />
        <MinProximityIntersection alarmDistance="0.03" contactDistance="0.02" />
        <DiscreteIntersection/>
        <DefaultContactManager name="Response" response="FrictionContact"/> -->

        <Node name="Floor">
            <EulerImplicit rayleighStiffness="0.1" printLog="false"  rayleighMass="0.1" />
            <CGLinearSolver threshold="1e-8" tolerance="1e-5" iterations="25"/>

            <MeshObjLoader name="loader" filename="mesh/floorFlat.obj"/>
            <MeshTopology src="@loader"/>
            <MechanicalObject name="mecha" src="@loader" template="Rigid3d" scale3d="10 1 10" translation="50 0 50" showObject="1"/>
            <UniformMass totalMass="10000.0"/>
            <UncoupledConstraintCorrection/>
            <OglModel name="visual" src="@loader" color="blue" scale3d="10 1 10" translation="50 0 50"/>
            <FixedConstraint indices='0 1 2 3'/>

            <Node name="Coll_Rec">
                <MeshTopology src="@../loader"/>
                <MechanicalObject src="@../loader" name="coll" scale3d="10 1 10" translation="50 0 50"/>

                <TTriangleModel/>
                <TLineModel/>
                <TPointModel/>
                <RigidMapping input="@.." output="@coll"/>
            </Node>   
        </Node>
    </Node>
    
    <Node name="CylinderScene">
<!--         <VisualStyle displayFlags="showBehaviorModels" />
        <FreeMotionAnimationLoop solveVelocityConstraintFirst="0"/>
        <LCPConstraintSolver maxIt="1000" tolerance="1e-6" mu="0.9"/>
        <DefaultPipeline depth="5" verbose="0" draw="0" />
        <BruteForceDetection name="N2" />
        <MinProximityIntersection alarmDistance="0.03" contactDistance="0.02" />
        <DiscreteIntersection/>
        <DefaultContactManager name="Response" response="FrictionContact"/> -->
        
        <Node name="Cylinder">
            <EulerImplicit rayleighStiffness="0.1" printLog="false"  rayleighMass="0.1" />
            <CGLinearSolver threshold="1e-8" tolerance="1e-5" iterations="25"/>

            <MeshObjLoader name="loader_cyl" filename="mesh/cylinder.obj"/>
            <MechanicalObject name="Cyl" src="@loader_cyl" template="Rigid3d" scale3d="0.8 0.8 0.8" translation="-30 100 -65"/>
            <UniformMass totalMass="10000.0"/>
            <UncoupledConstraintCorrection/>

            <Node name="Visu_Cyl">
                <OglModel name="visual_cyl" src="@../loader_cyl" color="green" scale3d="0.8 0.8 0.8"/>
                <RigidMapping input="@.." output="@visual_cyl"/>
            </Node>

            <Node name="Coll_Cyl">
                <MeshTopology src="@../loader_cyl"/>
                <MechanicalObject src="@../loader_cyl" name="coll_cyl" scale3d="0.8 0.8 0.8"/>

                <TTriangleModel/>
                <TLineModel/>
                <TPointModel/>
                <RigidMapping input="@.." output="@coll_cyl"/>
            </Node>
        </Node>   
    </Node>

    <DataExchange name="exchangeData1" template="vector<float>" from="@FloorScene/Floor/mecha.position" to="@CylinderScene/Cylinder/Cyl.position"/>
</Node>

Best

Hugo

[Hugo]

Dear @outtt

My apologies for this long silence! The start of 2020 is intense!

Let me first ask some further info. Do you really need the blood vessel to have an accurate mechanical behavior or are you mostly interesting in the interaction/grasping effect ?

In case you want to get a ‘realistic interaction’ only, the use of triangular FE model + bending springs might be sufficient.

In case you really need an advanced mechanical surface model (shell), I do have a good news: the shell plugin will soon be made open source. Beforehand, I need to clean it and go through some administrative steps. But it will be available freely!

Best wishes,

Hugo

[Hugo]

Hi guys!

I am writing you to give you some additional updates. On top of last year integration of SOFA within Unity3D, other independent developers are actively investigating the use of SOFA as the physics engine in Unreal Engine. Check out this latest video:

In case you are interested for collaborating, co-developping or consulting these indiedevs, do not hesitate to contact us.

Best wishes,

Hugo

[Hugo]

Hi @nguyenvanpho

SofaPython3 is not yet officially distributed with SOFA. However, you should already be able to download it and compile it with SOFA.

Which version of SOFA are you using?
Could you post the error/crash/warning message you have?
I would need a bit more info to assist you.

PS: you post image is not loaded properly

Best

Hugo

[Hugo]

Hi @joshuaf

Sorry for the “Christmas” silence!
For me the finger ms you are pointing to is working but with the same TetrahedronSetTopologyContainer error.

Could you give me the version of SOFA you are using and where you downloaded it from please?
Best,

Hugo

[Hugo]

the mesh seems to have some troubles. The TetrahedronSetTopologyContainer returns this:

[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [2, 120] in triangle 0
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [2, 120] in triangle 0
[WARNING] [TetrahedronSetTopologyContainer(container)] TrianglesAroundEdge buffer can't be created as EdgesInTriangle buffer creation failed.
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find triangle 0 [131, 125, 144] in tetrahedron 0
[ERROR]   [TetrahedronSetTopologyContainer(container)] Cannot find triangle 0 [131, 125, 144] in tetrahedron 0
[WARNING] [TetrahedronSetTopologyContainer(container)] TetrahedraAroundTriangle buffer can't be created as trianglesInTetrahedron buffer creation failed.

Could you try with other volumetric mesh of yours please?
Best

Hugo

[Hugo]

hi @joshuaf

Works fine for me (using another mesh because I don’t have the finger.vtk
Are you sure the file is containing tetrahedra ?
Does the mesh come from the SoftRobot plugin?

Hugo

[Hugo]

Hi @navyasri

Did you want to ask a related question? Anyway, do not hesitate to open a new topic (especially if it does not relate to this topic).
Best wishes,

Hugo

[Author]

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