MDSuite

MDSuite performs post-processing of particle-based (PB) molecular dynamics (MD) simulation data to compute physical observables and material properties and is implemented in Python.

Key Features:

• TensorFlow integration: Uses TensorFlow to perform computationally intensive analyses on simulation data.
• Data management (HDF5 and SQL): Stores and manages large simulation datasets using HDF5 and SQL databases.
• FAIR data principles: Organizes data processing according to FAIR (Findable, Accessible, Interoperable, Reusable) principles to promote reproducibility.
• Memory safety and parallelization: Implements memory-safe operations and parallelized computations to handle large datasets efficiently.
• GPU acceleration: Supports GPU acceleration to speed up analysis workflows.
• Extensive calculator suite: Provides 17 calculators that compute properties such as diffusion coefficients, thermal conductivity, viscosity, radial distribution functions, and coordination numbers.
• Modular object-oriented framework: Employs an object-oriented design that enables development and integration of new calculators and file-readers for different simulation software.

Scientific Applications:

• Extraction of system observables: Computes observables from MD trajectories that are difficult to obtain experimentally.
• Material properties characterization: Calculates transport and structural properties such as diffusion coefficients, thermal conductivity, and viscosity for materials research.
• Biological systems analysis: Analyzes particle-based simulation data relevant to biological system dynamics and interactions.
• Complex fluids studies: Enables investigation of structural and transport behavior in complex fluids via radial distribution functions and coordination numbers.

Methodology:

Computations are executed via TensorFlow with data stored in HDF5 and SQL; the implementation supports GPU acceleration, parallelized and memory-safe operations, and an object-oriented modular framework providing 17 calculators for specific property calculations (e.g., diffusion coefficients, thermal conductivity, viscosity, radial distribution functions, coordination numbers).