MicMec 1.0

The micromechanical model is a coarse-grained force field model to simulate the mechanical behaviour of crystalline materials on a large length scale. MicMec is the first implementation of that model. The theoretical groundwork was originally established in:

S. M. J. Rogge, “The micromechanical model to computationally investigate cooperative and
correlated phenomena in metal-organic frameworks,” Faraday Discuss., vol. 225, pp. 271–285, 2020.

MicMec is, essentially, a simulation package for coarse-grained, micromechanical systems. Its design is intentionally similar to Yaff, a simulation package for atomistic systems. In the process of building MicMec, the original micromechanical model was modified slightly, to ensure user friendliness, accuracy and flexibility. Recent changes and quality-of-life improvements are listed in the user guide and reference guide.

User Guide

This guide serves as an introduction to MicMec.

• 1. Installation
  • 1.1. Dependencies
  • 1.2. Installation
• 2. Creating micromechanical cell types
  • 2.1. Trajectory analysis
  • 2.2. PICKLE files
• 3. Constructing micromechanical systems
  • 3.1. Code-based construction
  • 3.2. GUI-based construction: the Micromechanical Model Builder
• 4. Performing simulations

Reference Guide

This guide is generated automatically based on the docstrings in the source code.

• 1. micmec – MicMec, the micromechanical model.
  • 1.1. micmec.log – Screen logger.
  • 1.2. micmec.system – Representation of a micromechanical system.
  • 1.3. micmec.utils – Auxiliary routines for system construction.
• 2. micmec.builder – The Micromechanical Model Builder.
  • 2.1. micmec.builder.builder_io – Input and output handling of the Micromechanical Model Builder.
• 3. micmec.pes – Micromechanical potential energy surfaces (PESs).
  • 3.1. micmec.pes.ext – C routines
  • 3.2. micmec.pes.mmff – MicMecForceField, the micromechanical force field.
  • 3.3. micmec.pes.nanocell – Micromechanical description of a single nanocell state.
  • 3.4. micmec.pes.nanocell_original – Micromechanical description of a single nanocell state (original).
  • 3.5. micmec.pes.nanocell_thesis – Micromechanical description of a single nanocell state (thesis).
  • 3.6. micmec.pes.nanocell_utils – Fixed parameters for the evaluation of a nanocell’s potential energy surface. DO NOT CHANGE.
• 4. micmec.sampling – Phase-space sampling.
  • 4.1. micmec.sampling.dof – Abstraction layer for degrees of freedom.
  • 4.2. micmec.sampling.iterative – Base class for iterative algorithms.
  • 4.3. micmec.sampling.npt – Barostats.
  • 4.4. micmec.sampling.nvt – Thermostats.
  • 4.5. micmec.sampling.opt – Geometry optimization.
  • 4.6. micmec.sampling.trajectory – Trajectory writers.
  • 4.7. micmec.sampling.utils – Auxiliary routines for initial velocities.
  • 4.8. micmec.sampling.verlet – The velocity Verlet algorithm.
• 5. micmec.analysis – Trajectory analysis.
  • 5.1. micmec.analysis.advanced – Advanced trajectory analysis routines.
  • 5.2. micmec.analysis.basic – Basic trajectory analysis routines.
  • 5.3. micmec.analysis.tensor – Auxiliary routines for tensors.
  • 5.4. micmec.analysis.utils – Auxiliary analysis routines.

Indices and tables

• Index

• Module Index

• Search Page