Martin Ganahl

User guide example for Small-molecule Protein Simulation broken

2

Hi there! First thank you for your great work here! I'm a newcomer to openmm and currently try to set up an MD simulation of a protein with a small...

Hi! Thanks for the great work here! I'm be interested in running an MD simulation of a protein-ligand complex, using espaloma for the ligand FF and a standard FF for...

Complex Tensor Contractions are unusually slow

1

Hi Devin, Thanks for this nice library! I'm currently testing the library, and I found the following: For real tensors, tblis is substantially faster than a contraction using dgemm for...

all_to_all with axis_index_group argument broken

5

Hi! I'm hitting some unexpected behaviour when using `all_to_all`. I'm trying to do partial swaps of a pmapped axis. The following code performes the parallel version of `np.arange(8).reshape(2,2,2).transpose((0,2,1)).reshape(4,2)`, and works...

sparse eigenvalue solvers

47

Hi! Our team is currently developing sparse symmetric and non-symmetric solvers in JAX (implicitly restarted arnoldi and lanzcos). I have it from hearsay that there are efforts to support this...

update contraction tutorials

6

We now also have Glen's contractor. We should add a tutorial for that

fix all pytorch tests

7

As of lately pytorch has complex number support. This means we have to fix the tests that were skipping pytorch on the ground that complex was not supported.

revert to `tensordot2` once `tf.matmul` is fixed

1

The `tf.matmul` bug documented at https://github.com/tensorflow/tensorflow/issues/52148 causes `tensordot2` to fail under certain circumstances. Once tensorflow fixes the bug on their side we should revert to using `tensordot2` in the `TensorflowBackend`.

orthogonalization for tensors

12

Initialization of orthogonal tensors with respect to a pivot