| analyticalSol | Class analytical solutions for the Physalis cage points |
| boundaryCond | Set outer boundary conditions for velocity |
| cage | Calculate coordinates of cage points and call the class analyticalSol to calculate the velocity boundary conditions at cage points |
| cageInit | Set velocity for cage points at the initial stage |
| divUStar | Calculate divergence of u* |
| exactSol | Set exact solutions of velocity and pressure for calculating accuracy |
| flowSolver | The actual flow solver |
| ghostPoint | Interpolate the ghost velocity points at the interface of two meshes |
| initCond | Set initial conditions |
| initStage | Calculate the initial stage using the velcity at cage points from cageInit |
| inputData | Read input file with a free format |
| LLSSolver | Linear Least Square Solver |
| NSSolver | Navier-Stokes equation Solver |
| outputData | Output velocity and pressure to files |
| PetscLinearSolver | Linear system solver |
| pressure | Pressure Poisson equation Solver |
| projectionMethod | Projection method solver |
| setDt | Set time increment dt for stability |
| uNew | Calculate the velocity at the next step |
| uStar | Calculate the predicted velocity u* |
| vorticity | Calculate vorticity |
1.5.6