softmatter:Basic Dynamical Simulation Methodology

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There are many different Dynamical Simulation Methods, integration schemes, thermostats, barostats, etc. however the basic methodology for setting up and running a simulation varies little.


1. Setting up the system

Initialize system parameters

  • Parameters such as σ, the characteristic size, number density (or box size), number of particles, temperature, timestep, etc.

Initialize particle positions

Select interaction potential

  • A continuous interaction potential needs to be chosen where there is an explicit form for the potential as a function of radial separation (U(r)) and force as a function of a radial separation (F(r)) where  F= - \mathcal{5} U . Common interaction potentials include The Lennard-Jones, Weeks-Chandler-Andersen, and Dzugutov potentials.

2. Calculate forces on each particle

  • Interactions are considered between every pair of particles in the system based on the previously chosen interaction potential. Algorithms have been developed to coarse grain this including the cell list and neighbor list routines.

3. Integrate equations of motion

4. Repeat

  • Go back to step 2, where forces are calcuated, and repeat the process.
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