.todo.md

monk

Todo

• Get rid of the scripts/snakemake, and just have python functions for more complex behaviors

  • Common analysis methods will be store in monk.methods
  • Move analysis runners totally into the workflows directory, using signac-flow

• Write a first pass at the forward flux code

  • Maybe do this for a brownian particle in a simple well first (without HOOMD) ✅
  • Then move to try this with a glassy particle
  • Compare FF and isoconfiguration estimates for free energy barrier

• Oscillatory shear simulations

  • Make some simple methods for driving and controlling the system
    • Continually updated sinusoidal shear (for thermal systems)
      • Implement plugin for the sinusoidal Variant object
    • Triangle-wave shear for athermal systems
  • signac managed workflows for these types of sims

• Mud stuff

  • Plots of shear rate vs stress for simple LJ system (athermal)

APS

• Generate simple isoconfigurational runs on the original MLJ data
  • Just 100 replicas for each temperature point
  • Use propensity for dynamics
  • No athermal quench, just thermal
  • Jump every 10 steps in data

Scratch

So maybe it's the