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Modelling tools

The Computing for Science (CS) group supports ILL scientists, students and visitors in a number of activities including data analysis, instrument simulation and sample simulation.

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Modelling tools

Multi-purpose simulation packages (from MSI - Molecular Simulations Incorporated - www.msi.com)

Cerius2 version 4.2MS (MSI)

VISUALIZER
for viewing and manipulating molecular models
CRYSTAL, AMORPHOUS and POLYMER BUILDERS
for constructing atomic and molecular models 
CRYSTAL, POWDER_INDEXING, POWDER_SOLVE for calculating diffraction patterns from molecular (crystal) models and for refining models from diffraction data
OPEN_FORCE_FIELD,  FORCE_FIELD_EDITOR, CFF, COMPASS, DYNAMICS and MINIMIZER
for setting-up force fields, loading MSI-specific force fields,and running minimisation and molecular dynamicscalculations
SORPTION
for simulating the adsorption of molecules in porous media
HP_MORPHOLOGY, MORPHOLOGY SURFACE_BUILDER SURFACE_DOCKER
for simulating crystal morphology and growth
POLYMORPHfor predicting crystal structures and polymorphs starting from a molecular description (crystallographers should not
worry, this does not replace doing diffraction - yet!)
MOPAC_INTERFACE, CASTEP, DMOL3-SOLID_STATE GAUSSIAN_INTERFACE
for performing and analysing quantum chemistry calculations (see below)

Materials Studio version 1.2 (MSI) windows version of Cerius2

COMPASS
sa MSI-specific force field, developed from ab initio calculations
DISCOVER
for setting-up force fields and running minimisation and molecular dynamics calculations  
REFLEX_PLUSpowder diffraction utilities (indexing, Pawley fitting, Monte Carlo space searching for atomiccoordinates, Rietveld refinement) 
VISUALIZER for viewing and manipulating molecular models

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Quantum chemistry codes

MOPAC
semi-empirical Hartree-Fock based code for molecules and clusters up to ~200 atoms (available in Cerius2)
GAMESS-UK(http://www.dl.ac.uk/TCSC/Software/GAMESS/main.html) Hartree-Fock based ab initio code for molecules and (small) clusters, like Gaussian but cheaper!
CASTEP
plane wave based DFT code for periodic systems (available in Cerius2)
VASP
(http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html) plane wave based DFT code for periodic systems
SIESTA
(http://www.uam.es/departamentos/ciencias/fismateriac/siesta) atomic orbital based DFT code for periodic systems, offering linear scaling
DMOL3
atomic orbital based DFT code for periodic systems (available in Cerius2)

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Force field codes

CHARMM(Chemistry at HARvard Macromolecular Mechanics - mir.harvard.edu)
DL-POLY(www.dl.ac.uk/TCSC/Software/DL_POLY/main.html)
GROMOS(http://www.tik.ee.ethz.ch/~md/hammsoft.htm)
AMBER(http://www.amber.ucsf.edu/amber/amber.html)
TINKER(http://dasher.wustl.edu/tinker/) can use various force field parameter sets
from, for example, CHARMM and AMBER

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Analysis programs

MDANSE

MDANSE (Molecular Dynamics Analysis for Neutron Scattering Experiments) is a python application designed for computing properties that can be directly compared with neutron scattering experiments such as the coherent and incoherent intermediate scattering functions and their Fourier transforms, the elastic incoherent structure factor, the static coherent structure factor or the radial distribution function.

It can also compute quantities such as the mean-square displacement, the velocityautocorrelation function as well as its Fourier Transform (the so-called vibrational density of states) enlarging the scope of the program to a broader range of physico-chemical properties.


Most of MDANSE calculations can be applied to the whole system or to arbitrary subsets that can be defined in the graphical interface while less common selections can be specified via the command-line interface. MDANSE is written in Python and currently works on Linux, MacOS and Windows.

CLIMAX a program developed by Don Kearley for the analysis of molecular vibrations and simulation of neutron scattering vibrational spectra. CLIMAX can use and refine empirical force-fields and can read Gaussian
ab initio and MOPAC (semi-empirical) output files. A manual is available. (send an Email to the author)
A limited version of the program (http://www.isis.rl.ac.uk/molecularSpectroscopy/aclimax/) has been
developed in EXCEL and allows the neutron spectra to be calculated from normal modes, without subsequent force constant refinement. This approach is generally adequate when periodic DFT codes are used to determine normal modes.
PHONON (http://wolf.ifj.edu.pl/phonon/) a program for calculating phonon dispersion curves and density of states for crystals from empirical force constants or Hellmann-Feynmann forces, generated by periodic DFT codes like CASTEP, VASP, SIESTA etc.

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