Refactor/consolidate neq engine#114

Merged

jesperswillem merged 11 commits into

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refactor/consolidate-neq-engine

Jul 24, 2026

Commits on Jul 23, 2026

fold non-equilibrum executable into qdyn, toggled by md input parameters generated by the python part -- QligFEP
David-Araripe
committed
change neq-related python part to use the qdyn binary
David-Araripe
committed
update neq analyzer to write the calculated values to the mapping.json, similar to the equilibrium analyzer
David-Araripe
committed
simplify the analysis modules using a shared diagnostics method across both analyzers (neq and equilibrium). Also, remove duplicated method from analyze_FEP caused by merge conflicts during rebase
David-Araripe
committed
1. lint qligfep module, and 2. change the MPI binding to add the --map-by core to avoid cases where `ranks` > `available cores` caused by OpenMPI in some instances of resource allocation from Slurm
David-Araripe
committed
improve module IO to catch MPI failure messages & add tests
David-Araripe
committed
make serial qdyn exit non-zero on abnormal termination and improve running templates to correctly halt the run if it crashes
David-Araripe
committed
fix test with wrong assumption
David-Araripe
committed

Commits on Jul 24, 2026