fennol.md

FeNNol Molecular Dynamics Module

This module provides molecular dynamics simulation capabilities using machine learning potentials. The main entry point is through the dynamic.py module which implements the fennol_md command.

Modules: dynamic: Main MD simulation engine and parameter documentation integrate: Integration schemes and system initialization
initial: System setup and model loading thermostats: Temperature control algorithms barostats: Pressure control algorithms colvars: Collective variable calculations spectra: Infrared spectrum computation utils: Utility functions for restarts and coordinate wrapping

For complete parameter documentation, see dynamic.py or use: help(fennol.md.dynamic)

Example usage: from fennol.md.dynamic import config_and_run_dynamic config_and_run_dynamic(Path("input.fnl"))

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 1"""
 2FeNNol Molecular Dynamics Module
 3
 4This module provides molecular dynamics simulation capabilities using machine learning potentials.
 5The main entry point is through the `dynamic.py` module which implements the fennol_md command.
 6
 7Modules:
 8    dynamic: Main MD simulation engine and parameter documentation
 9    integrate: Integration schemes and system initialization  
10    initial: System setup and model loading
11    thermostats: Temperature control algorithms
12    barostats: Pressure control algorithms
13    colvars: Collective variable calculations
14    spectra: Infrared spectrum computation
15    utils: Utility functions for restarts and coordinate wrapping
16
17For complete parameter documentation, see `dynamic.py` or use:
18    help(fennol.md.dynamic)
19
20Example usage:
21    from fennol.md.dynamic import config_and_run_dynamic
22    config_and_run_dynamic(Path("input.fnl"))
23"""