diff --git a/README.md b/README.md index 07b9f52..4b06c24 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ A generic proxy-app toolbox for state-of-the-art molecular dynamics algorithms -## Build instructions for the lammps variant +## Build instructions Properly configure your building by changing `config.mk` file. The following options are available: @@ -32,19 +32,32 @@ Configurations for GROMACS MxN optimization scheme: Configurations for CUDA: - **USE\_CUDA\_HOST\_MEMORY:** Use CUDA host memory to optimize host-device transfers. +When done, just use `make` to compile the code. You can clean intermediate build results with `make clean`, and all build results with `make distclean`. You have to call `make clean` before `make` if you changed the build settings. -## Configuration +## Usage -Currently all settings apart from the options described below are hard-coded in `main.c`. +Use the following command to run a simulation: -## Run the benchmark - -Without any options 200 steps with system size 32x32x32 is used. - -The default can be changed using the following options: +```bash +./MD-Bench-- [OPTION]... ``` + +Where `TAG` and `OPT_SCHEME` correspond to the building options with the same name. +Without any options, a Copper FCC lattice system with size 32x32x32 (131072 atoms) over 200 time-steps using the Lennard-Jones potential (sigma=1.0, epsilon=1.0) is simulated. + +The default behavior and other options can be changed using the following parameters: +``` +-p : file to read parameters from (can be specified more than once) +-f : force field (lj or eam), default lj +-i : input file with atom positions (dump) +-e : input file for EAM -n / --nsteps : set number of timesteps for simulation -nx/-ny/-nz : set linear dimension of systembox in x/y/z direction +-r / --radius : set cutoff radius +-s / --skin : set skin (verlet buffer) +--freq : processor frequency (GHz) +--vtk : VTK file for visualization +--xtc : XTC file for visualization ```