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Atom and moltype strong types - #581

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atom-and-moltype-strong-types
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Atom and moltype strong types#581
97gamjak wants to merge 4 commits into
devfrom
atom-and-moltype-strong-types

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@97gamjak

@97gamjak 97gamjak commented Sep 8, 2026

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@pq-perf-bot

pq-perf-bot Bot commented Sep 8, 2026

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⚡ Performance (instruction count) — 🎉 improvement: forceKernel -26.30%

per-benchmark breakdown
benchmark base Ir PR Ir Δ
bondedForces 38.25M 38.25M +0.00%
boxTransforms 10.67M 10.67M +0.00%
constraints 11.03M 11.06M +0.29%
coulombKernel 5.80M 5.80M +0.00%
forceKernel 13.54M 9.98M -26.30% 🎉
integrator 32.91M 32.91M -0.00%
interWater 1679.92M 1689.12M +0.55%
kinetics 8.55M 8.55M -0.00%
linearAlgebra 2.08M 2.08M +0.00%
nonCoulombPairs 5.48M 5.48M +0.00%
shiftVector 5.81M 5.81M +0.00%
virial 10.04M 10.04M -0.00%

Deterministic callgrind instruction counts vs the base branch; gated at ±2%. Not wall-clock.

@codecov

codecov Bot commented Sep 8, 2026

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Codecov Report

❌ Patch coverage is 94.02985% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.34%. Comparing base (c524e3a) to head (60f0111).

Files with missing lines Patch % Lines
src/constraints/mShake.cpp 37.50% 5 Missing ⚠️
src/input/intraNonBondedReader.cpp 71.42% 2 Missing ⚠️
src/molsys/moleculeType.cpp 80.00% 2 Missing ⚠️
include/molsys/molecule.hpp 0.00% 0 Missing and 1 partial ⚠️
src/input/guffDatReader.cpp 96.96% 0 Missing and 1 partial ⚠️
src/molsys/simulationBox.cpp 90.90% 0 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##              dev     #581      +/-   ##
==========================================
- Coverage   91.44%   91.34%   -0.11%     
==========================================
  Files         322      322              
  Lines       14628    14601      -27     
  Branches     4915     4930      +15     
==========================================
- Hits        13377    13337      -40     
- Misses       1169     1176       +7     
- Partials       82       88       +6     

☔ View full report in Codecov by Harness.
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  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@97gamjak 97gamjak linked an issue Sep 8, 2026 that may be closed by this pull request
@97gamjak
97gamjak requested a review from ape33 September 8, 2026 16:22
@97gamjak
97gamjak requested a review from galjos September 10, 2026 13:51
- Updated AngleForceField, BondForceField, and DihedralForceField tests to use parameter structs for setting equilibrium values and force constants.
- Modified AngleType, BondType, DihedralType, and JCouplingType tests to utilize parameter structs for improved clarity and maintainability.
- Adjusted test assertions to reflect the new parameter struct access methods.
- Removed unnecessary includes and improved code formatting for better readability.
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strong types for atomtype, extatomtype and moltype

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