Universally Adaptable Multiscale Molecular Dynamics (UAMMD) ver 2.0

See the wiki for more info!
You can find videos on the youtube channel http://bit.ly/2r5WoOn

DESCRIPTION

Raul P. Pelaez 2018-2022. (raul.perez(at)uam.es)

A C++14+ header-only fast generic multiscale CUDA Molecular Dynamics framework made with moduarity, expandability and generality in mind. UAMMD is intended to be hackable and copy pastable.

Although "Molecular Dynamics" is part of the name,the UAMMD framework allows for much more than that. To this moment multiple integrators are implemented allowing it to perform:

-Molecular dynamics (MD)  
-Brownian Dynamics  (BD)  
-Brownian Hydrodynamics (BDHI)  
-Dissipative Particle Dynamics (DPD)  
-Smoothed Particle Hydrodynamics (SPH)  
-Metropolis Monte Carlo (MC)   
-Lattice Boltzmann (LBM)(WIP)  
-Fluctuating Hydrodynamics (coupled with particles with Immerse Boundary Method (IBM))

Building blocks are provided for the user to construct a certain simulation. Most are highly templated to ease adaptability.

For example, there is no harmonic trap module, but you can write a simple functor (directly in device code!) stating that each particle should experiment a force when it is trying to leave the box. Then you can pass this functor to the ExternalForces module. Similar things can be achieved with a bonded force, an interaction that needs to trasverse a neighbour list, an nbody interaction...

Hop on to the examples folder for an introduction or check the documentation for more information.

Currently Implemented

See the documentation page at https://uammd.readthedocs.io for a full list of available modules.

USAGE

UAMMD does not need to be compiled separatedly (it is header only).

Some special flags might be needed to compile codes including with certain UAMMD headers, see Compiling UAMMD.
Here you have a short example of how a typical UAMMD code looks like:

//Ideal brownian particles
#include"uammd.cuh"
#include"Integrator/BrownianDynamics.cuh"
using namespace uammd;
int main(int argc, char * argv[]){
	int numberParticles = 1e5;
	auto pd = make_shared<ParticleData>(numberParticles);
	{
		auto pos = pd->getPos(access::cpu, access::write);
		std::generate(pos.begin(), pos.end(), [&](){ return make_real4(sys->rng.uniform3(-0.5, 0.5), 0);});	
	}
	BD::EulerMaruyama::Parameters par;
	par.temperature = 1.0;
	par.viscosity = 1.0;
	par.hydrodynamicRadius = 1.0;
	par.dt = 0.1;
	auto bd = make_shared<BD::EulerMaruyama>(pd, par);
	for(int i = 0; i<numberSteps; i++){
		bd->forwardTime();
	}
	sys->finish();
	return 0;
}

Drop by the examples folder to get started with UAMMD or go to the wiki.

DEPENDENCIES

Depends on:

1. CUDA 9.x+                                :   https://developer.nvidia.com/cuda-downloads

Some modules make use of certain NVIDIA libraries included with CUDA:

1. cuBLAS
2. cuFFT

Some modules also make use of lapacke and cblas (which can be replaced by mkl).
Apart from this, any dependency is already included in the repository under the third_party folder.
See Compiling UAMMD in the documentation for more information.

ACKNOWLEDGMENTS

UAMMD is being developed at the Departamento de Física Teórica de la Materia Condensada of Universidad Autónoma de Madrid (UAM) under supervision of Rafael Delgado-Buscalioni. Acknowledgment is made to the Donors of the American Chemical Society Petroleum Research Fund (PRF# 54312-ND9) for support of this research and to Spanish MINECO projects FIS2013- 47350-C05-1-R, FIS2013-50510-EXP and mostly FIS2017-86007-C3-1-P.

Acknowledgment is made to NVIDIA Corporation for their GPU donations.

Collaborators

Raul P. Pelaez is the main developer of UAMMD.

Other people that have contributed to UAMMD (thanks!):

Marc Melendez Schofield
Sergio Panzuela
Nerea Alcazar
Pablo Ibañez Freire (https://github.com/PabloIbannez)
Salvatore Assenza

fbusabiaga / UAMMD