Sassena is a highly scalable parallelized software for calculating neutron and xray scattering intensities from all-atomic molecular dynamics simulations. It enables scientific scattering calculations only attainable through massively large parallel computers. The development of sassena is a consequence of the need to calculate scattering diagrams for systems with thousands of atoms and millions of time steps. These calculations require enormous computing power in the range of thousands of cores and up to terabytes of memory. As a side effect, the overall time for calculating scattering of small systems and short trajectories can be significantly reduced through the use of parallel computers.
The direct computation of scattering diagrams based on (all-atomic) molecular dynamics trajectories allows reconciliation of simulations with experiment. Scattering diagrams also provide a powerful tool to investigate structural and dynamical properties of simulated molecular systems by reducing the amount of information into meaningful structural and dynamical fingerprints.
Sassena was inspired by pre-existing software and integrates their capabilities:
SASSIM (SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins, F. Merzel and J. C. Smith, 2002, Acta Cryst.. D58, p. 242-249)
SERENA (SERENA: a program for calculating X-ray diffuse scattering intensities from molecular dynamics trajectories, Micu A.M., Smith J.C., 1995, Computer Physics Communications, 91 (1-3), pp. 331-338.).
nMoldyn 2, G R. Kneller, V Keiner, M Kneller and M Schiller, "nMoldyn, a program package for the calculation and analysis of neutron scattering spectra from MD simulations" Comp. Phys. Comm., vol. 91, (1995), 191-214., T Róg, K Murzyn, K Hinsen and G R. Kneller, "nMoldyn : A Program Package for a Neutron Scattering Oriented Analysis of Molecular Dynamics Simulations" J. Comp. Chem. no. 5, vol. 24, (2003), 657-667.
The design goal of the sassena software suite is to enable scientific scattering calculations which are only attainable through the use of massively parallel computers. However, the software also represents a great educational tool for investigating structural and dynamical properties of molecular systems. For this reason this websites contains a collection of tutorials, in-depth information and hosts the sassena user community.
Though the focus of the software is scalability, work is underway to increase single-node performance and optimize IO access.
The inaugural paper is online (http://dx.doi.org/10.1016/j.cpc.2012.02.010) and the source code is available free of charge and open source.
If you use Sassena for your calculations please cite the following reference:
B. Lindner and J.C. Smith, 2012, "Sassena — X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers", Comp. Phys. Comm., Volume 183, Issue 7, Pages 1491–1501, http://dx.doi.org/10.1016/j.cpc.2012.02.010
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\ :sup:`coh`\ (Q,t)
* incoherent intermediate scattering function I\ :sup:`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 <https://www.ks.uiuc.edu/Research/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
************
An `AppImage is provided <https://codebase.helmholtz.cloud/DAPHNE4NFDI/sassena/-/releases>`_ that can run on Linux out of the box when executed (no installation needed). For optimal performance, Sassena can be compiled on the target machine, e.g. on Ubuntu 24.04:
To contribute, please create a feature branch from the develop branch and merge back into it.
*****************************
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 <http://dx.doi.org/10.1016/j.cpc.2012.02.010>`_
