Sassena

Sassena is a program to calculate X-ray and neutron scattering patterns from Molecular Dynamics simulations in the Born approximation.

Description

The full documentation is currently hosted on https://daphne4nfdi.pages.hzdr.de/sassena (access restrictions apply).

Sassena can calculate:

• structure factor S(Q)
• coherent intermediate scattering function I^coh(Q,t)
• incoherent intermediate scattering function I^inc(Q,t)
• elastic incoherent structure factor EISF(Q)

Filetypes:

• Sassena can read pdb files for atom type definition and dcd files containg the trajectory. For trajectory conversion, use e.g. VMD.
• The computation has to be defined by the user in an xml file
• Sassena writes the output into an hdf file

Orientational averages are calculated explicitly using a Monte Carlo scheme. It is possible to define subsets of atoms or frames that the computation should run on.

Sassena has a command-line interface and can be run across many CPUs using MPI.

Installation

You can choose to either use a pre-built binary of Sassena, which contains all the required libraries or build the project yourself from source. For more information, visit the documentation.

AppImage

An AppImage is provided that can run on Linux (x64, without CUDA support) out of the box when executed (no installation needed). To use it, download the AppImage from the releases page, mark it as an executable and run it from the command-line:

chmod +x Sassena.AppImage
./Sassena.AppImage # --config scatter.xml etc.
# or to use mpi:
mpirun -n 16 ./Sassena.AppImage --config scatter.xml

Compiling from Source

For optimal performance (e.g. using target-specific registers, CUDA), Sassena can be compiled on the target machine, e.g. on Ubuntu 24.04:

sudo apt install build-essential cmake ninja-build git\
 openmpi-bin libblas-dev liblapack-dev\
 libxml2-dev libhdf5-dev zlib1g-dev libfftw3-dev\
 libboost-regex-dev libboost-mpi-dev\
 libboost-thread-dev libboost-serialization-dev libboost-system-dev\
 libboost-filesystem-dev libboost-program-options-dev
git clone https://codebase.helmholtz.cloud/DAPHNE4NFDI/sassena.git
cd sassena
git submodule update --init --recursive
cmake --preset=rel-cpu # or rel-cuda if you want to build with CUDA
cd build-rel-cpu
ninja

Contributing

To contribute, please create a feature branch from the develop branch and add your changes and then create a merge request onto the develop branch. The repo uses rebasing workflow, so you may need to rebase your changes onto the develop branch before the merge can be completed.

For further information, please see CONTRIBUTING.rst.

Notable upstream repositories

https://github.com/camm/sassena

https://github.com/benlabs/sassena

Citation

If you use Sassena for your calculations please cite

Benjamin Lindner and Jeremy C. Smith: "Sassena — X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers", Comp. Phys. Comm. 183/7 (2012) 1491, DOI: 10.1016/j.cpc.2012.02.010