Inelastic and quasi-elastic neutron scattering (INS and QENS, respectively) spectroscopy are useful tools for probing molecular dynamics in materials. Atomistic simulations, particularly molecular dynamics (MD) simulations are being used increasingly for analysis of these data. However, predicting neutron observables from MD trajectories is not straightforward. A number of operations, such as calculations of velocity auto- and cross-correlation functions, Fourier transformations and convolutions with instrument parameters are required to calculate neutron observables that can be compared directly with experimental data.
Some of these steps were implemented in the open source MDANSE (Molecular Dynamics Analysis of Neutron Scattering Experiments). This software has interface with more than ten MD codes including some ab-initio MD codes, such as CASTEP, VASP, DMOL, Gromacs, DL_POY, CHARMM, LAMMPS, PBD, DFTB etc. showing potential to be used widely.
In the current project, we have taken the initiative to upgrade the MDANSE code so that it would be easy to use and compile, written in python3 and dependencies transferred from NetCDF to HDF in addition to reducing dependencies on some old software, such as Pyro. Individual scripts from this developed utility can be accessed by users for their particular use without using the full code.
The sustainable software and utility will be an asset to the future neutron scattering community for atomistic simulations and neutron scattering data analysis.
Downloads
Download latest executables (version 1.5.1 released 3rd August, 2022) :
Windows10 : Windows_executable.zip
MacOS (intel/M1) : MacOS_executable.zip
Ubuntu (22.04) : ubuntu-22.04_installer.zip
Ubuntu (21.04) : ubuntu-21.04_installer.zip
Ubuntu (20.04) : ubuntu-20.04_installer.zip
Ubuntu (18.04) : ubuntu-18.04_installer.zip
Nightly Builds
Download executables (1.5.2-beta version for testing, Last updated 9th February, 2023)
Windows10 : Windows_executable_nightly.zip
MacOS (intel only) : MacOS executable_nightly.zip
Ubuntu (22.04) : ubuntu-22.04_installer_nightly.zip
Ubuntu (21.04) : ubuntu-21.04_installer_nightly.zip
Ubuntu (20.04) : ubuntu-20.04_installer_nightly.zip
Ubuntu (18.04) : ubuntu-18.04_installer_nightly.zip
Download executables (compiled 25th October, 2022)
Windows10 : Windows_executable_nightly.zip
MacOS (intel/M1) : MacOS executable_nightly.zip
Ubuntu (22.04) : ubuntu-22.04_installer_nightly.zip
Ubuntu (21.04) : ubuntu-21.04_installer_nightly.zip
Ubuntu (20.04) : ubuntu-20.04_installer_nightly.zip
Ubuntu (18.04) : ubuntu-18.04_installer_nightly.zip
User Guide is available here : RAL-TR-2022-003.pdf
A more up-to-date online Users Guide is available here.
The update about MDANSE software will be available in MDANSE github page.
The training materials of MDANSE school will be available here.
Citing MDANSE
If you find MDANSE useful for your research, please cite the following paper in your publications:
- MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations, G. Goret, B. Aoun, and E. Pellegrini, Journal of Chemical Information and Modeling 2017 57 (1), 1-5, [DOI: 10.1021/acs.jcim.6b00571]
Acknowledgements
MDANSE is a modern interface
for analysis of molecular dynamics trajectories from a wide range of simulation
packages. It started as a fork of version 3 of the nMOLDYN program. The main transition from nMoldyn to MDANSE is the change in GUI and addition of the molecular viewer. Other changes have been added subsequently will be ound in the Changelog at Github..
nMOLDYN was originally developed by Gerald Kneller in 1995 and subsequently also by Konrad Hinsen, Tomasz Rog, Krzysztof Murzyn, Slawomir Stachura, and Eric Pellegrini. MDANSE uses nMOLDYN3 for the most computationally intensive analyses, and also code from the libraries MMTK and ScientificPython, in order to reduce dependencies and thus facilitate installation.
For more information on the history and successive developments of nMoldyn, see:
- “nMOLDYN: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations"; G. R. Kneller, V. Keiner, M. Kneller, M. Schiller; Comp. Phys. Comm. 91, 191-214 (1995).
- “nMoldyn: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations"; T. Róg, K. Murzyn, K. Hinsen, G. R. Kneller; J. Comput. Chem. 24, 657-667 (2003).
- “nMoldyn3: Using task farming for a parallel spectroscopy-oriented analysis of molecular dynamics simulations"; K. Hinsen, E. Pellegrini, S. Stachura, G. R. Kneller; J. Comput. Chem. 33, 2043-2048 (2012).
The latest version of nMOLDYN3 can be found at http://dirac.cnrs-orleans.fr/nMOLDYN.html.
We are grateful to all the people who have contributed to nMOLDYN and MDANSE. Apart from the main developers mentioned above, we would like to acknowledge explicitly the contributions of Bachir Aoun, Vania Calandrini, Paolo Calligari, Gael Goret and Remi Perenon.
In the course of its journey the MDANSE poject has received a number of finantial supports. The MDANSE project is supported by Ada Lovelace Centre, ISIS Neutron and Muon Source, Science and Technology Facilities Council, UKRI, and the Institut Laue-Langevin (Grenoble, France). Past financial support from the French Agence Nationale de la Recherche (ANR) through contracts No. ANR-2010-COSI-001-01 and ANR-06-CIS6-012-01, and the Horizon 2020 Framework Programme of the European Union under project number 654000 is also acknowledged.
To know more about the project and discuss your requirements from the software contact Sanghamitra Mukhopadhyay (sanghamitra.mukhopadhyay@stfc.ac.uk).
This project is supported by Ada Lovelace Centre.
