How rkailasham-group/computational-soft-matter works
This repository is a computational soft-matter research project: it prepares particle configurations, runs Active Brownian Particle simulations, and analyzes trajectories against diffusion theory or collective-clustering measures. The principal workflow is initial configuration → simulation → saved trajectory → analysis/visualization. The README also documents 2D reciprocal-swimmer and 3D single-particle MSD studies; the sampled 2D simulate.py only writes a one-frame starting snapshot, so its connection to the plot’s expected trajectories is not established here. Collective-analysis wiring is based on the sampled scripts; some excerpts are partial.
Main entry points: 3D_Single_Sphere/simulate.py 3D Simulator · msd.py MSD Extractor · Multiple_Colloidal_Spheres/simulate.py Collective Simulator · 2D_Disk/simulate.py Disk Snapshot
Components 17
2D Disk Study
- Disk Snapshot
Prince/Active-Brownian-Particles/2D_Disk/simulate.py - Disk GSD
- MSD Plot
Prince/Active-Brownian-Particles/2D_Disk/plot_msd.py
3D Single Sphere
- Sphere Snapshot
Prince/Active-Brownian-Particles/3D_Single_Sphere/box.py - 3D Simulator
Prince/Active-Brownian-Particles/3D_Single_Sphere/simulate.py - 3D Trajectories
- MSD Extractor
Prince/Active-Brownian-Particles/3D_Single_Sphere/msd.py - MSD Data
- Theory Comparison
Prince/Active-Brownian-Particles/3D_Single_Sphere/vis.py
Collective Spheres
- Dense Snapshot
Prince/Active-Brownian-Particles/Multiple_Colloidal_Spheres/box.py - Collective Simulator
Prince/Active-Brownian-Particles/Multiple_Colloidal_Spheres/simulate.py - Dense Trajectories
- Cluster Dynamics
Prince/Active-Brownian-Particles/Multiple_Colloidal_Spheres/cluster_analysis.py - Cluster Statistics
Prince/Active-Brownian-Particles/Multiple_Colloidal_Spheres/average_cluster_size.py - Cluster Variance
Prince/Active-Brownian-Particles/Multiple_Colloidal_Spheres/variance.py
Simulation Engine
- HOOMD-blue
Other components
- Researcher
Connections 25
- Researcher → Disk Snapshot: starts
- Disk Snapshot → Disk GSD: writes snapshot
- Researcher → MSD Plot: runs analysis
- MSD Plot → Disk GSD: reads trajectories
- Researcher → Sphere Snapshot: creates state
- Sphere Snapshot → 3D Trajectories: writes snapshot
- Researcher → 3D Simulator: starts runs
- 3D Simulator → 3D Trajectories: reads input, writes output
- 3D Simulator → HOOMD-blue: uses simulation API
- Researcher → MSD Extractor: runs extraction
- MSD Extractor → 3D Trajectories: reads trajectories
- MSD Extractor → MSD Data: writes MSD
- Researcher → Theory Comparison: plots comparison
- Theory Comparison → MSD Data: reads MSD
- Researcher → Dense Snapshot: creates state
- Dense Snapshot → Dense Trajectories: writes snapshot
- Researcher → Collective Simulator: starts run
- Collective Simulator → Dense Trajectories: reads input, writes output
- Collective Simulator → HOOMD-blue: uses simulation API
- Researcher → Cluster Dynamics: runs analysis
- Cluster Dynamics → Dense Trajectories: reads trajectories
- Researcher → Cluster Statistics: runs summary
- Cluster Statistics → Dense Trajectories: reads trajectories
- Researcher → Cluster Variance: runs analysis
- Cluster Variance → Dense Trajectories: reads trajectories