Plectoneme-Solenoid Transition about pyelastica

[armantekinalp]

Hello,

We have not included that case in our examples for PyElastica yet. For the paper, it was simulated using our Cpp code. You can also set this case by yourself with PyElastica. What you have to do is:

1. Set up your client file create simulation class, rod object, append rod object to simulation, etc. You can refer to one of the example cases in the examples directory. Also, I suggest you visit our website for more explanation.

2. For the Plectonme-Solenoid test case, you need two boundary conditions. One boundary condition is already part of PyElastica which is OneEndFixedRod.. You need to write a second boundary condition. It should be rotating the other end of the rod throughout the twist time. To write a new boundary condition you can refer to already written boundary condition in elastica/boundary_condition.py . I suggest you to especially look at HelicalBucklingBC.

3. Finally, you need to add a force at the end of the rod. For that, you can use EndPointForces class. One example use case of this class is given in examples/TimoshenkoBeamCase/timoshenko.py.

Let me know if you have further questions.

[HogeLab]

Thank you !　
I also want to try the simulation in the case of adding a torque at the end of the rod , but a module like EndPointTorques dosen't exit.
Do I need to make that module by myself ?

[armantekinalp]

Yes you need to write the class. Couple of reminders,

1. Make sure you derived new forcing class for EndPointTorques from NoForces class. Otherwise simulation will throw an error.

2. Add your torque calculation in apply_torque class method.

3. We are storing external torques in material frame, so if you are applying torque in lab frame of reference then you need to multiply computed torques with director_collection.

class EndPointTorques(NoForces):
    def __init__(self, torque_start, torque_end):

        self.torque_start = torque_start # defined in global frame, shape(3,1)
        self.torque_end= torque_end # defined in global frame, shape(3,1)

   def apply_forces(self, system, time: np.float = 0.0):
        return

   def apply_torques(self, system, time: np.float = 0.0):

        system.external_torques[...,0] += system.director_collection[...,0] @ self.torque_start 
        system.external_torques[...,-1] += system.director_collection[...,-1] @ self.torque_end 
      

[HogeLab]

Thank you very much.

[HogeLab]

I can't find Self-contact setting that corresponds to useSelfContact in elastica++. Where is it ? Will it be programmed in the future?

[armantekinalp]

Yes it hasn't implemented yet. It will be implemented in future.

[HogeLab]

Thanks.