Physical validation reference
physical_validation is a package aimed at testing results obtained
by molecular dynamics simulations for their physical validity.
Note
The physical validation methodology has been described in Merz PT, Shirts MR (2018), Testing for physical validity in molecular simulations. PLoS ONE 13(9): e0202764. https://doi.org/10.1371/journal.pone.0202764
Note
We are always looking to enlarge our set of tests. If you are a MD user or developer and have suggestions for physical validity tests missing in this package, we would love to hear from you! Please consider getting in touch with us via our github repository.
User guide:
Examples:
Data format and parsers:
- Creation of
SimulationDataobjects - Data contained in
SimulationDataobjects- Units:
SimulationData.unitsof typeUnitData - Ensemble:
SimulationData.ensembleof typeEnsembleData - System:
SimulationData.systemof typeSystemData - Observables:
SimulationData.observablesof typeObservableData - Atom trajectories:
SimulationData.trajectoryof typeTrajectoryData - Time step:
SimulationData.dtof typefloat
- Units:
Package reference:
- physical_validation package
- physical_validation.data subpackage
- physical_validation.data.simulation_data module
- physical_validation.data.unit_data module
- physical_validation.data.ensemble_data module
- physical_validation.data.trajectory_data module
- physical_validation.data.observable_data module
- physical_validation.data.system_data module
- physical_validation.data.parser module
- physical_validation.data.gromacs_parser module
- physical_validation.data.flatfile_parser module
- physical_validation.util subpackage