Molecular Dynamics

Implements Velocity Verlet using a Lennard Jones force field. Outputs PDB files. Supports domain decomposition on OpenMP. Offers a SYCL backend-too (but no domain decomposition there yet).

Building instructions

With hipSYCL

Use the supplied script to get a version of hipSYCL and build the simulator with it.

chmod u+x build.sh
./build.sh

With Intel(R) oneAPI or LLVM:

Just use clang++ (with SYCL support) or dpcpp as the default C++ compiler:

mkdir -p build ; cd build
CXX={clang++|dpcpp} cmake .. -DSYCL={CPU|HIP|CUDA}
make main
./main ../particule.xyz

For DPC++/Clang, eventually change the target flags in CMakeLists.txt in DPCPP_FLAGS and select the device with the env variable SYCL_DEVICE_FILTER=....

Sequential/Reference version:

Set -DSYCL to OFF.

Benchmark

Pass -DBUILD_BENCH=ON to cmake and the target to build is benchmark_lennard_jones or benchmark_decompose.

Execution

To run the simulation with domain decomposition run:

./main particule.xyz -decompose

Otherwise, to run it on SYCL (domain decomposition not supported yet), replace decompose by sycl. Omitting the flag will run the default simulation (C++) without domain decomposition.