2. Input File

The following sections provide a concise overview of various input parameters used to control the behaviour of the code at run time.

• 2.1. The input file
  • 2.1.1. Using the input file
  • 2.1.2. Key value pairs
  • 2.1.3. Unused key value pairs
• 2.2. Simulation parameters
  • 2.2.1. System size and parallel decomposition
  • 2.2.2. Simulation time steps
  • 2.2.3. Fuild parameters
• 2.3. The free energy
  • 2.3.1. Available free energies
  • 2.3.2. Symmetric binary fluid
  • 2.3.3. Brazovskii smectics
  • 2.3.4. Polar active gels
  • 2.3.5. Liquid crystals
  • 2.3.6. Liquid crystal emulsion
  • 2.3.7. Ternary free energy
  • 2.3.8. Electrokinetic free energy
• 2.4. Lees Edwards SPBCs
  • 2.4.1. Lees Edwards sliding periodic boundary conditions
• 2.5. Colloids
  • 2.5.1. Introducing colloids
  • 2.5.2. Single colloid initialisation
  • 2.5.3. Ellipsoidal particles
  • 2.5.4. Many colloid initialisation at random
  • 2.5.5. Colloid interactions
  • 2.5.6. Liquid crystal anchoring at colloid surfaces
• 2.6. Plane walls
  • 2.6.1. Plane boundary walls
  • 2.6.2. Wetting at plane boundary walls
  • 2.6.3. Anchoring for liquid crystals at plane walls
• 2.7. Porous Media
  • 2.7.1. Standard porous media structures
  • 2.7.2. Porous media structures from file
• 2.8. Open boundaries
  • 2.8.1. Open boundary conditions and walls
  • 2.8.2. Hydrodynamic open boundaries
  • 2.8.3. Open boundaries for composition
  • 2.8.4. Restarting with open boundary conditions
• 2.9. Order Parameters
  • 2.9.1. Order parameter initialisations
  • 2.9.2. Tensor order parameter
  • 2.9.3. Order parameter gradients
• 2.10. Viscosity Models
  • 2.10.1. Newtonian Fluid
  • 2.10.2. Arrhenius
• 2.11. Force on the fluid
  • 2.11.1. Body forces
  • 2.11.2. Constant body forces
  • 2.11.3. Local forces from the thermodynamic sector
• 2.12. Parallelism
  • 2.12.1. Distributed memory parallelism
  • 2.12.2. Threaded parallelism via OpenMP
  • 2.12.3. Threaded parallelism for GPU
  • 2.12.4. Timing