The periodic wrapper and operator data generator to be used with PVFMM
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InstallationInstructions.md
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README.md

README.md

PeriodicFMM

The C++/C/Fortran/Python wrapper for flexibly periodic FMM and operator data generator to be used with PVFMM.

The flexibly periodic KIFMM algorithm is described in:

  • Yan, W. & Shelley, M. Flexibly imposing periodicity in kernel independent FMM: A multipole-to-local operator approach. Journal of Computational Physics 355, 214–232 (2018).

The flexibly periodic Stokeslet Image algorithm is described in:

  • Yan, W. & Shelley, M. Universal image systems for non-periodic and periodic Stokes flows above a no-slip wall. Journal of Computational Physics 375, 263–270 (2018).

Please cite them if you find this package useful.

Dependency: The C++ template library Eigen is necessary to compile the test driver main.cpp. The wrapper class itself (FMMWrapper.h/.cpp) does not rely on Eigen.

Capability:

FMMWrapper.h/.cpp

  • Singular Stokeslet kernel force -> velocity
  • Regularized Stokeslet kernel force + torque + spreading -> velocity + angular velocity

With NONE/PX/PXY/PXYZ periodicity

FMMWrapperWall2D.h/.cpp

  • Singular Stokeslet kernel force -> velocity above a no slip wall

With NONE/PX/PXY periodicity

How-To:

0. Follow InstallationInstructions.md to setup the toolchain.

1. Generate the M2L matrix

Go to folders in M2LLaplace or M2LStokes and modify the Makefile to use the correct c++ compiler and the correct path to Eigen library header files.

After compilation, type:

XXX.X p > ./M2LYYYaD3Dpb

where XXX.X is the name of the executable, YYY is the name of the kernel (Stokes, LaplaceCharge, LaplaceDipole, etc), p is the discretization number for KIFMM, 'a' is periodic dimension, and 'b' is the point number for the equiv surface. 'b' controls the tradeoff between accuracy and cost. 'b=10' gives single precision and 'p=16' gives double precision, roughly. For exmaple, M2L2D3Dp8 means doubly periodic in 3D space with p=8. See FMMWrapper.cpp for details.

For example

localhost:periodicfmm wyan$ cd ./M2LStokes/2D3D/
localhost:2D3D wyan$ ./Stokes2D3D.X 8 > ./M2LStokes2D3Dp8

The executable also solves a tiny test problem to check the accuracy after the M2L operator is calculated. At the end of the above execution process, you should see something like:

localhost:2D3D wyan$ tail ./M2LStokes2D3Dp8
-4.527578312263358384e-11
Usample M2L total: 1.567028182748916532e+00
 1.769944468765771717e-10
-4.527578312263358384e-11
Usample Ewald: 1.567028149573803653e+00
-4.150067072042485956e-19
 0.000000000000000000e+00
error 3.317511287903585071e-08
 1.769944472915838697e-10
-4.527578312263358384e-11

2. Perform test and calculations

Copy those M2LYYYaD3Dpb files for Stokes kernel to the subfolder /pdata/ in $PVFMM_DIR, remove any extra lines to make sure the M2L files start with "i j value" lines like:

localhost:2D3D wyan$ head ./M2LStokes2D3Dp8
0 0 -8.963371808378797212e+00
0 1 -1.614059953274547965e+01
0 2 2.183755414811182050e+01
0 3 6.150120972933304841e+00

The correct folder structure should look like:

localhost:2D3D wyan$ cd $PVFMM_DIR
localhost:pvfmm wyan$ ls ./pdata/M2LStokes*
./pdata/M2LStokes1D3Dp10 ./pdata/M2LStokes2D3Dp10 ./pdata/M2LStokes3D3Dp10
./pdata/M2LStokes1D3Dp12 ./pdata/M2LStokes2D3Dp12 ./pdata/M2LStokes3D3Dp12
./pdata/M2LStokes1D3Dp14 ./pdata/M2LStokes2D3Dp14 ./pdata/M2LStokes3D3Dp14
./pdata/M2LStokes1D3Dp16 ./pdata/M2LStokes2D3Dp16 ./pdata/M2LStokes3D3Dp16
./pdata/M2LStokes1D3Dp6  ./pdata/M2LStokes2D3Dp6  ./pdata/M2LStokes3D3Dp6
./pdata/M2LStokes1D3Dp8  ./pdata/M2LStokes2D3Dp8  ./pdata/M2LStokes3D3Dp8

The wrapper files are located in the folder 'FMM':

PeriodicFMM/ $ ls ./FMM
FMMWrapper.cpp  FMMWrapper.h  FMMWrapper.o  FMMWrapperWall2D.cpp  FMMWrapperWall2D.h  LaplaceCustomKernel.hpp
PeriodicFMM/ $ 

The test-driving routines are located in the folder 'ModuleTest'

PeriodicFMM/ $ ls ./ModuleTest/
StokesFMM3D  StokesFMMWall2D  MakefileInc.mk
PeriodicFMM/ $ 

Modify the file MakefileInc.mk properly.

To run the demo and tests for Stokes 3D periodic FMM:

PeriodicFMM/ $ cd ModuleTest/StokesFMM3D/
StokesFMM3D/ $ make
make: 'TestStokes3D.X' is up to date.
StokesFMM3D/ $ TestStokes3D.X --help

to get command line options.

To run the demo and tests for Stokes 3D periodic FMM above a wall:

PeriodicFMM/ $ cd ModuleTest/StokesFMMWall2D/
StokesFMMWall2D/ $ make
make: 'TestStokesWall2D.X' is up to date.
StokesFMMWall2D/ $ ./TestStokesWall2D.X --help

to get command line options.

This test driver demonstrates how to use the wrapper FMM class and can perform tests for FreeSpace, SP, DP, TP in 3D space, for random & chebyshev points, with OpenMP & MPI.

Warning

This wrapper only works with the new_BC branch of my fork of PVFMM.