- 1. Introduction
- 2. Installation
- 3. Setting up the system
- 4. Setting up particles
- 4.1. Overview of the relevant Python classes
- 4.2. Adding particles
- 4.3. Accessing particle properties
- 4.4. Interacting with groups of particles
- 4.5. Deleting particles
- 4.6. Iterating over particles and pairs of particles
- 4.7. Exclusions
- 4.8. Create particular particle configurations
- 4.9. Virtual sites
- 4.10. Particle number counting feature
- 4.11. Self-propelled swimmers
- 5. Running the simulation
- 6. Non-bonded interactions
- 6.1. Isotropic non-bonded interactions
- 6.1.1. Tabulated interaction
- 6.1.2. Lennard-Jones interaction
- 6.1.3. Generic Lennard-Jones interaction
- 6.1.4. Lennard-Jones cosine interaction
- 6.1.5. Smooth step interaction
- 6.1.6. BMHTF potential
- 6.1.7. Morse interaction
- 6.1.8. Buckingham interaction
- 6.1.9. Soft-sphere interaction
- 6.1.10. Membrane-collision interaction
- 6.1.11. Hat interaction
- 6.1.12. Hertzian interaction
- 6.1.13. Gaussian
- 6.1.14. DPD interaction
- 6.1.15. Thole correction
- 6.2. Anisotropic non-bonded interactions
- 6.1. Isotropic non-bonded interactions
- 7. Bonded interactions
- 8. Electrostatics
- 9. Magnetostatics / Dipolar interactions
- 10. System manipulation
- 11. Single particle forces (constraints)
- 12. Lattice Boltzmann
- 12.1. Setting up a LB fluid
- 12.2. Checkpointing LB
- 12.3. LB as a thermostat
- 12.4. Reading and setting properties of single lattice nodes
- 12.5. Removing total fluid momentum
- 12.6. Output for visualization
- 12.7. Choosing between the GPU and CPU implementations
- 12.8. Electrohydrodynamics
- 12.9. Using shapes as lattice Boltzmann boundary
- 13. Analysis
- 13.1. Direct analysis routines
- 13.1.1. Energies
- 13.1.2. Momentum of the System
- 13.1.3. Minimal distances between particles
- 13.1.4. Particles in the neighborhood
- 13.1.5. Particle distribution
- 13.1.6. Cylindrical Average
- 13.1.7. Radial distribution function
- 13.1.8. Structure factor
- 13.1.9. Center of mass
- 13.1.10. Moment of inertia matrix
- 13.1.11. Gyration tensor
- 13.1.12. Pressure
- 13.1.13. Stress Tensor
- 13.1.14. Local Stress Tensor
- 13.1.15. Chains
- 13.2. Observables and correlators
- 13.3. Accumulators
- 13.4. Cluster analysis
- 13.1. Direct analysis routines
- 14. Input and Output
- 15. Online-visualization
- 16. Advanced Methods
- 16.1. Creating bonds when particles collide
- 16.2. Swimmer Reactions
- 16.3. Lees-Edwards boundary conditions
- 16.4. Immersed Boundary Method for soft elastic objects
- 16.5. Object-in-fluid
- 16.6. Electrokinetics
- 16.7. Particle polarizability with thermalized cold Drude oscillators
- 16.8. Reaction Ensemble
- 17. Under the hood
- 18. Contributing
- 19. Appendix
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