duello 0.1.6__tar.gz → 0.2.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (61) hide show
  1. {duello-0.1.6 → duello-0.2.0}/.vscode/settings.json +3 -1
  2. {duello-0.1.6 → duello-0.2.0}/.zenodo.json +7 -1
  3. duello-0.2.0/CLAUDE.md +9 -0
  4. {duello-0.1.6 → duello-0.2.0}/Cargo.lock +1267 -359
  5. {duello-0.1.6 → duello-0.2.0}/Cargo.toml +14 -7
  6. duello-0.2.0/PKG-INFO +5 -0
  7. duello-0.1.6/PKG-INFO → duello-0.2.0/README.md +61 -28
  8. duello-0.1.6/examples/calvados3/calvados3.yaml → duello-0.2.0/examples/calvados3/topology.yaml +7 -1
  9. {duello-0.1.6 → duello-0.2.0}/examples/lookup.rs +3 -3
  10. {duello-0.1.6 → duello-0.2.0}/pyproject.toml +1 -1
  11. {duello-0.1.6 → duello-0.2.0}/scripts/calvados3.sh +1 -1
  12. {duello-0.1.6 → duello-0.2.0}/scripts/cppm.sh +3 -3
  13. duello-0.2.0/src/backend/cpu.rs +70 -0
  14. duello-0.2.0/src/backend/gpu.rs +621 -0
  15. duello-0.2.0/src/backend/mod.rs +78 -0
  16. duello-0.2.0/src/backend/simd.rs +294 -0
  17. duello-0.2.0/src/energy.rs +208 -0
  18. {duello-0.1.6 → duello-0.2.0}/src/icoscan.rs +90 -35
  19. {duello-0.1.6 → duello-0.2.0}/src/icosphere.rs +114 -53
  20. {duello-0.1.6 → duello-0.2.0}/src/icotable.rs +38 -37
  21. {duello-0.1.6 → duello-0.2.0}/src/lib.rs +1 -0
  22. {duello-0.1.6 → duello-0.2.0}/src/main.rs +209 -37
  23. {duello-0.1.6 → duello-0.2.0}/src/sample.rs +30 -10
  24. duello-0.2.0/src/shaders/energy.wgsl +224 -0
  25. {duello-0.1.6 → duello-0.2.0}/src/spherical.rs +1 -5
  26. {duello-0.1.6 → duello-0.2.0}/src/structure.rs +29 -30
  27. {duello-0.1.6 → duello-0.2.0}/src/table.rs +8 -11
  28. {duello-0.1.6 → duello-0.2.0}/src/vertex.rs +4 -1
  29. {duello-0.1.6 → duello-0.2.0}/src/virial.rs +11 -12
  30. duello-0.2.0/topology.yaml +41 -0
  31. duello-0.1.6/README.md +0 -169
  32. duello-0.1.6/examples/calvados3/topology.yaml +0 -8
  33. duello-0.1.6/examples/cppm/virial-integration.ipynb +0 -484
  34. duello-0.1.6/pdb2xyz/.python-version +0 -1
  35. duello-0.1.6/pdb2xyz/README.md +0 -0
  36. duello-0.1.6/pdb2xyz/main.py +0 -222
  37. duello-0.1.6/pdb2xyz/pyproject.toml +0 -7
  38. duello-0.1.6/src/energy.rs +0 -112
  39. duello-0.1.6/uv.lock +0 -256
  40. {duello-0.1.6 → duello-0.2.0}/.cargo/config.toml +0 -0
  41. {duello-0.1.6 → duello-0.2.0}/.github/dependabot.yml +0 -0
  42. {duello-0.1.6 → duello-0.2.0}/.github/workflows/rust.yml +0 -0
  43. {duello-0.1.6 → duello-0.2.0}/.gitignore +0 -0
  44. {duello-0.1.6 → duello-0.2.0}/.vscode/extensions.json +0 -0
  45. {duello-0.1.6 → duello-0.2.0}/.vscode/launch.json +0 -0
  46. {duello-0.1.6 → duello-0.2.0}/.zed/settings.json +0 -0
  47. {duello-0.1.6 → duello-0.2.0}/LICENSE +0 -0
  48. {duello-0.1.6 → duello-0.2.0}/assets/atoms.yml +0 -0
  49. {duello-0.1.6 → duello-0.2.0}/assets/convert-calvados3.ipynb +0 -0
  50. {duello-0.1.6 → duello-0.2.0}/assets/duello-logo.png +0 -0
  51. {duello-0.1.6 → duello-0.2.0}/assets/illustration.png +0 -0
  52. {duello-0.1.6 → duello-0.2.0}/examples/calvados3/4lzt.xyz +0 -0
  53. {duello-0.1.6 → duello-0.2.0}/examples/cppm/cppm-p00.xyz +0 -0
  54. {duello-0.1.6 → duello-0.2.0}/examples/cppm/cppm-p18.xyz +0 -0
  55. {duello-0.1.6 → duello-0.2.0}/examples/cppm/topology.yaml +0 -0
  56. {duello-0.1.6 → duello-0.2.0}/examples/lazy_static.rs +0 -0
  57. {duello-0.1.6 → duello-0.2.0}/examples/notebook/interpolation-error.ipynb +0 -0
  58. {duello-0.1.6 → duello-0.2.0}/examples/notebook/plot_potential.py +0 -0
  59. {duello-0.1.6 → duello-0.2.0}/scripts/colab.ipynb +0 -0
  60. {duello-0.1.6 → duello-0.2.0}/src/fibonacci.rs +0 -0
  61. {duello-0.1.6 → duello-0.2.0}/src/report.rs +0 -0
{duello-0.1.6 → duello-0.2.0}/.vscode/settings.json RENAMED
@@ -96,5 +96,7 @@
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  "other": true,
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  "comments": false,
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  "strings": true
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- }
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+ },
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+ "python-envs.defaultEnvManager": "ms-python.python:conda",
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+ "python-envs.pythonProjects": []
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  }
{duello-0.1.6 → duello-0.2.0}/.zenodo.json RENAMED
@@ -9,7 +9,8 @@
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  }
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  ],
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  "contributors": [
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- {"type": "Researcher", "name": "Isabel Vinterbladh", "orcid": "0009-0007-0801-2611"}
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+ {"type": "Researcher", "name": "Isabel Vinterbladh", "orcid": "0009-0007-0801-2611"},
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+ {"type": "Researcher", "name": "Harold Hatch", "orcid": "0000-0003-2926-9145"}
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  ],
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  "keywords": [
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  "statistical thermodynamics",
@@ -23,6 +24,11 @@
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  "scheme": "url",
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  "identifier": "https://github.com/mlund/duello",
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  "relation": "isSupplementTo"
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+ },
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+ {
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+ "scheme": "doi",
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+ "identifier": "10.26434/chemrxiv-2025-0bfhd",
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+ "relation": "isSupplementTo"
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  }
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  ],
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  "access_right": "open",
duello-0.2.0/CLAUDE.md ADDED
@@ -0,0 +1,9 @@
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+ - Performance benchmarks should be based on:
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+ ~~~
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+ cd examples/calvados3/
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+ duello scan -1 4lzt.xyz -2 4lzt.xyz --rmin 26 --rmax 60 --dr 0.5 --top topology.yaml --resolution 0.5 --cutoff 150 --molarity 0.02`
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+ ~~~
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+ - Avoid lenghty Rust functions
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+ - Reduce nested code with helper functions
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+ - Prefer *why* over *what* in code comments
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+ - For git commits, be brief and don't add (co)-authorship