UAMMD: https://github.com/RaulPPelaez/uammd

This code allows to call UAMMD's PSE module from a python script to compute the product of the mobility with a certain vector (usually forces acting on particle positions).
You can read about PSE here: https://github.com/RaulPPelaez/UAMMD/wiki/BDHI-PSE

You need UAMMD and pybind11, both of which are included in this repository as git submodules. Remember to clone recursively with:

git clone --recursive https://github.com/RaulPPelaez/UAMMD_PSE_Python

You need the CUDA toolkit installed, I tested up to the latest version at the moment (CUDA 11).

The PSE module uses cufft, cublas, lapacke and cblas which need to be available during compilation. CuFFT and CuBLAS should be available as part of the CUDA installation.

Just run make and thats it. Notice that you may need to modify it with the appropiate paths of your systems (mainly the location of nvcc and python).
The Makefile uses the python-config utility and assumes that is called $(PYTHON)-config, change it otherwise.
You may enable debug mode by adding -DUAMMD_DEBUG -g -G to the compilation line, also increasing the verbosity in the makefile will help track down any runtime issues.
The Makefile also assumes nvcc is in the PATH but you can easily change it to point to wherever it is.

Do not try to modify the parameters after you have created the UAMMD object as it will have no effect whatsoever in it.
Mdot expects positions and forces to be in a one dimensional array with interleaved pattern such that positions = [x1, y1, z1, x2, y2, z2...]. Same goes for the output, which must have the correct size (3*N) when passed to Mdot.

import uammd
numberParticles = 20000;
L=120.0;
par = uammd.PSEParameters(psi=0.3, viscosity=1.0, hydrodynamicRadius=1.0, tolerance=1e-4, box=uammd.Box(L,L,L));
pse = uammd.UAMMD(par, numberParticles);
...
pse.computeHydrodynamicDisplacements(positions, forces, MF, temperature = 1.0, prefactor = 1.0)

The function computeHydrodynamicDisplacements computes the full hydrodynamic displacements (including the deterministic and stochastic ones). If the "forces" argument is ommited only the stochastic contribution is computed. On the other hand, setting temperature=0 will result in only the deterministic part being computed. The prefactor affects the stochastic part, the result MF will be MF = Mobility*forces + prefactor*sqrt(2*temperature*Mobility)*dW).

PSE uses Ewald splitting, with a Near and Far field contribution. Each part of the deterministic computation can be computed separatedly with

pse.MdotNearField(positions, forces, MF)
pse.MdotFarField(positions, forces, MF)

Finally, the shearStrain parameter allows to use sheared boxes.

The module can also be called from C++ by including uammd_interface.h. See example.cpp.