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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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Rafael Ravedutti 2022-09-29 12:39:09 +02:00
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A generic proxy-app toolbox for state-of-the-art molecular dynamics algorithms 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: 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: Configurations for CUDA:
- **USE\_CUDA\_HOST\_MEMORY:** Use CUDA host memory to optimize host-device transfers. - **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 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. 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 ```bash
./MD-Bench-<TAG>-<OPT_SCHEME> [OPTION]...
Without any options 200 steps with system size 32x32x32 is used.
The default can be changed using the following options:
``` ```
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 <string>: file to read parameters from (can be specified more than once)
-f <string>: force field (lj or eam), default lj
-i <string>: input file with atom positions (dump)
-e <string>: input file for EAM
-n / --nsteps <int>: set number of timesteps for simulation -n / --nsteps <int>: set number of timesteps for simulation
-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction -nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction
-r / --radius <real>: set cutoff radius
-s / --skin <real>: set skin (verlet buffer)
--freq <real>: processor frequency (GHz)
--vtk <string>: VTK file for visualization
--xtc <string>: XTC file for visualization
``` ```