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13.0 3.0 1.0 642.74 MB

Implementation of the Reference Interaction-Site Model (RISM) equation

License: MIT License

Python 11.67% Makefile 0.11% Just 0.14% Rust 84.09% Shell 3.51% HTML 0.46%
chemistry computational-science scientific-computing solvation-structure rism ornstein-zernike molecular-liquids liquids atomic-liquids computational-chemistry

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drmaruyama

pyrism's Issues

Travis CI Security Breach Notice

MolSSI is reaching out to every repository created from the MolSSI Cookiecutter-CMS with a .travis.yml file present to alert them to a potential security breach in using the Travis-CI service.

Between September 3 and September 10 2021, the Secure Environment Variables Travis-CI uses were leaked for ALL projects and injected into the publicly available runtime logs. See more details here. All Travis-CI users should cycle any secure variables/files, and associated objects as soon as possible. We are reaching out to our users in the name of good stewards of the third-party products we recommended and might still be in use and provide a duty-to-warn to our end-users given the potential severity of the breach.

We at MolSSI recommend moving away from Travis-CI to another CI provider as soon as possible. The nature of this breach and the way the response was mis-handled by Travis-CI, MolSSI cannot recommend the Travis-CI platform for any reason at this time. We suggest either GitHub Actions (as is used from v1.5 of the Cookiecutter-CMS) or some other service offered on GitHub.

If you have already addressed this security concern or it does not apply to you, feel free to close this issue.

This issue was created programmatically to reach as many potential end-users as possible. We do apologize if this was sent in error.

0.4.0 Feature List

Future work feature list that I hope for pyRISM to have:

  • An actual logo (this would be nice)
  • Custom array data structures (this would track equivalent sites and symmetry reduced matrices)
  • Rewrite with Faer-rs
  • MPI (or at least better use of Rayon)

0.3.1 checklist

Checklist of features being added to 0.3.1

  • Lambda cycling (removed this from Rust implementation, slipped my mind to put it back in)
  • Better long output (currently doesn't work on some systems; overall looks janky. Tables are better.)
  • working PSE-n closure (currently a half-finished macro)
  • LMV solver Pushed to later release
  • MDIIS Refactor
  • Better reporting on solver information (solution times, iterations, etc. will be better for analysis in the long run)
  • Developer docs (or the start there of)
  • Comprehensive test suite for benchmarking

Symmetry reduction

Wrote a little quick RISM script in python for testing modifications quickly. Implemented symmetry reduction, I will implement this into 0.4.0

LMV solver

I've written the skeleton for the LMV solver in the lmv_dev branch and ideally it should be working and yet the outer cycle loop seems to diverge (while the inner cycle NR loop converges really quickly... maybe too quickly).

I don't have much time to address and spend more time on this at the moment, but leaving this issue for myself or anyone else interested in RISM and numerical methods.

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