edmondztt / fsd

Fast Stokesian Dynamics

Fast Stokesian Dynamics (FSD)

Original authors: Andrew M. Fiore, James W. Swan (MIT)

Note: The original FSD code contains a few minor errors in the lubrication and mobility calculations. Also, there was a bug causing memory leaks in the preconditioner. This version fixes these issues and tries to improve the overall performance and clarity.

A brief summary of the main files is given below. Deterministic hydrodynamics:

• Stokes.cc : C++ module to set up the method and run the integrator
• Stokes.cu : Driver function for integration
• Integrator.cu : Integrator wrappers, RK2, RFD, etc.
• Lubrication.cu : Near-field resistance (lubrication) functions (RFU, RFE, RSU, RSE)
• Solvers.cu : Methods to perform required matrix inversions
• Saddle.cu : Saddle point multiplication and solution
• Mobility.cu : Far-field mobility calculations
• Precondition.cu : Build the saddle point and near-field Brownian preconditioners
• Wrappers.cuh : C++ wrapper definitions for CUSP operations
• Stokes_ResistanceTable.cc : Values for pre-computed tabulation of lubrication functions
• Stokes_SparseMath.cc : Initialization and setup of variables required for sparse operations

Brownian motion:

• Brownian_FarField.cu : Methods to compute the far-field Brownian displacements
• Brownian_NearField.cu : Methods to compute the near-field Brownian forces

Auxiliary functions:

• Helper_Stokes.cu : Helper functions for two-step Stokes integrator
• Helper_Integrator.cu : Helper functions to simplify code in Integrator.cu
• Helper_Saddle.cu : Helper functions for saddle point matrix calculations
• Helper_Mobility.cu : Helper functions for mobility calculations in Mobility.cu
• Helper_Precondition.cu : Helper functions for preconditioning calcualtions
• Helper_Brownian.cu : Helper functions used in Brownian_FarField.cu and Brownian_NearField.cu
• Helper_Debug.cu : Functions for debugging and code checking, printing output, etc.

Brief summary of file dependency (not listed, but all files depend on their helpers, e.g. Mobility.cu depends on Helper_Mobility.cu)

• Stokes.cu : Integrator.cu
• Integrator.cu : Brownian_FarField.cu Brownian_NearField.cu Lubrication.cu Solvers.cu
• Mobility.cu : Helper_Mobility.cu
• Brownian_FarField.cu : Mobility.cu
• Brownian_NearField.cu : Lubrication.cu Preconditioner.cu
• Solvers.cu : Saddle.cu Wrappers.cuh
• Saddle.cu : Mobility.cu Lubrication.cu

Reference

Fiore, A. M., & Swan, J. W. (2019). Fast Stokesian dynamics. Journal of Fluid Mechanics, 878, 544-597.