v0.2.1

Release Note (version 0.2.1)

Developer Note

Contact model between two different rods and rod with itself is implemented.
Testing the contact model is done through simulations. These simulation scripts can be found under
RodContactCase.
However, in future releases we have to add unit tests for contact model functions to test them and increase code coverage.

Notable Changes

• #31: Merge contact model to master PR #40 in public
• #46: The progress bar can be disabled by passing an argument to integrate.
• #48: Experimental modules are added to hold functions that are in test phase.

Release Note

Click to expand

• Rod-Rod contact and Rod self contact is added.
• Two example cases for rod-rod contact is added, i.e. two rods colliding to each other in space.
• Two example cases for rod self contact is added, i.e. plectonemes and solenoids.
• Progress bar can be disabled by passing an argument to integrate function.
• Experimental module added.
• Bugfix in callback mechanism

hot fix: PyPi does not include reset memory block functions

This commit fixes the issue of PyPi not recognizing the reset functions for memory block.

v0.2.0

Release Note (version 0.2)

Developer Note

Good luck! If it explode, increase nu. 🤣 If it doesn't explode, thoroughly check for the bug.

Notable Changes

• #84: Block implementation
• #75: Poisson ratio and definition of modulus PR #26 in public
• #95: MuscularFlagella example case is added
• #100: ExportCallBack is added to export the rod-data into file.
• #109: Numpy-only version is now removed. Numba-implementation is set to default.
• #112: Save and load implementation with the example are added.

Release Note

Click to expand

• Block structure is included as part of optimization strategy.
• Different Poisson ratio is supported.
• Contributing guideline is added.
• Update readme
• Add MuscularFlagella example case
• Minimum requirement for dependencies is specified.
• Shear coefficient is corrected.
• Connection index assertion fixed.
• Remove numpy-only version.
• Save/Load example

Enhancement: Shear modulus and Poisson ratio warnings

• Soft changes are done for rod initialization. If user does not provides shear modulus then warning messages will be raised and shear modulus will be computed based on Poisson Ratio.

• We changed the test scripts to test new warning messages.

• Old test scripts are updated such that warning messages won't be raised.

• Examples are updated such that warning messages won't be raised.

Bugfix: interaction (plane friction) model

This release contains:

• Interaction (plane friction) model has a bug which results causing continuum snake speed to be higher.
• Continuum snake example updated according to our recent paper Zhang et. al 2021.

PyElastica v0.1.0.post3 release

This release fixes two bugs in the factory_function and Numba version of _rotate function.

PyElastica v0.1.0.post2 release

This release of PyElastica uses the Python package numba to enable just in time compilation leading to a ~8x speedup over the previous version. Numba is not required to run PyElastica and if numba is not installed, PyElastica will defualt to the non-numba implementation. As such, if you wish to take advantage of the speed-up afforded by numba, please be sure to install it separately.

Future releases of PyElastica will require numba and we will no longer be maintaining the non-numba code beyond this release.

We have also included an example script for visualizing PyElastica simulations using POVray. This script is located in the examples folder (examples/visualization).

(This post-release fixes a bug which appears with new version of Numba. In new versions of Numba jitclass is imported from numba.experimental and import path was wrong in PyElastica. Since we are not using jitclass we removed all jitclass import statements from the code base.)

PyElastica v0.1.0.post1 release

This release of PyElastica uses the Python package numba to enable just in time compilation leading to a ~8x speedup over the previous version. Numba is not required to run PyElastica and if numba is not installed, PyElastica will defualt to the non-numba implementation. As such, if you wish to take advantage of the speed-up afforded by numba, please be sure to install it separately.

Future releases of PyElastica will require numba and we will no longer be maintaining the non-numba code beyond this release.

We have also included an example script for visualizing PyElastica simulations using POVray. This script is located in the examples folder (examples/visualization).

(This post-release fixes a bug in the setup.py file to allow the package to properly install)

PyElastica v0.1.0 release

This release of PyElastica uses the Python package numba to enable just in time compilation leading to a ~8x speedup over the previous version. Numba is not required to run PyElastica and if numba is not installed, PyElastica will defualt to the non-numba implementation. As such, if you wish to take advantage of the speed-up afforded by numba, please be sure to install it separately.

Future releases of PyElastica will require numba and we will no longer be maintaining the non-numba code beyond this release.

We have also included an example script for visualizing PyElastica simulations using POVray. This script is located in the examples folder (examples/visualization).

PyElastica setup file import problem

This release fixes a problem in setup file, which was preventing pip to install all the sub packages of PyElastica.