SOFTWARE FOR
Computational Materials and Molecular Science
Software for Computational Materials and Molecular Sciences allows scientists to implement developed theory and solutions for scientific and technological challenges. It enables the prediction and understanding of material properties through simulations and various calculations.
ACDC – an adaptive kinetic Monte Carlo program to study diffusion in solid state materials
CAPABILITIES
ACDC is an adaptive kinetic Monte Carlo program to study diffusion in solid state materials. ACDC offers material chemistry simulations and interface to SchNet machine learned potentials.
TRAINING INFORMATION
STFC does not currently provide training for this software.
ACCESS
ACDC is expected to be released under BSD 3-Clause licence, which will make it free to download, compile and run. The licence is currently awaiting approval.
Aiida-mlip – reproducible workflows and full data provenance for janus-core package within the Aiida framework
CAPABILITIES
Aiida-mlip offers reproducible workflows and full data provenance for janus-core package within the Aiida framework. It allows scientists to create complex workflows for modelling in materials science that are reproducible and reusable with minimal or no changes to the code.
TRAINING INFORMATION
STFC provides online tutorials, that can be run via google colab, or on your machine. Code has been used at CCP5 Summer School advanced courses too. Please do not hesitate to contact the team via github issues if you need help.
ACCESS
ALC_EQCM – a post-processing software for Electrochemical Quartz Crystal Microbalance (EQCM) measurements
CAPABILITIES
ALC_EQCM is a post-processing software for Electrochemical Quartz Crystal Microbalance (EQCM) measurements. It automatises the generation of atomistic models compatible with stoichiometric solutions and provides quality-controlled input files for a variety of Density Functional Theory (DFT) codes. It also introduces a new workflow to bridge the gap between experimental and computational electrochemistry.
TRAINING INFORMATION
ALC_EQCM training documents and tutorials are available here. For more training information, contact Dr Ivan Scivetti.
ACCESS
This software is available via GitHub. This program performs post-processing of EQCM data to the purpose of electrochemical characterisation and building of atomistic models compatible with experiments.
ALC_Shapespyer – a Python driven toolchain and API library that automates generation and simulation of atomistic or coarse-grain molecular aggregates
CAPABILITIES
ALC_Shapespyer is a Python driven toolchain and API library that automates generation and simulation of atomistic or coarse-grain molecular aggregates.
It supports and complement SAS experiments by providing numerical simulation and analysis workflows tailored for validating experiment-inspired models against computer simulations.
TRAINING INFORMATION
Comprehensive training documents are available here.
In-person tutorial sessions for students and users as part of the ISIS SANS training courses are also available. Contact Dr Andrey Brukhno for further information.
ACCESS
This software is open–source and available here.
ALC_SUTOR – Python-based workflow software which generates Cumulative Electron Cross-Section Probabilities (CECCP) files
CAPABILITIES
ALC_SUTOR is a Python-based workflow software. It generates Cumulative Electron Cross-Section Probabilities (CECCP) files which can be used as input for Monte Carlo simulations to study the trajectories of electrons in materials and molecules.
TRAINING INFORMATION
Documentation and tutorials are available here: GitHub – stfc/ALC_SUTOR.
Training on ALC_SUTOR has been previously delivered. Please contact Dr Paolo Trevisanutto to express your interest in additional training.
ACCESS
This software is available via GitHub.
ALC_TRAJECTORY – orientational anisotropies and transfers correlations of atomic systems from trajectories generated with Molecular Dynamics simulations
CAPABILITIES
ALC_TRAJECTORY computes orientational anisotropies and transfer correlations of atomic systems from trajectories generated with Molecular Dynamics simulations. It identifies chemistry changes along the MD trajectory, computes orientational anisotropies, transfers correlation functions, and offers a new tool to support 2D and Fourier Transform Infrared experiments.
TRAINING INFORMATION
ALC_TRAJECTORY training resources are available here.
ACCESS
This software is available via GitHub.
Automated potential development (APD) workflow
CAPABILITIES
APD workflow offers automated development of interatomic potentials, requiring only the input of material and temperature range. It fully automates the setup and analysis of jobs, scheduling, the monitoring of all tasks, and generates relevant graphs, figures, and tables of phonons.
A Python-based workflow for guiding and automating the entire pipeline of developing interatomic potentials— from generating density functional theory (DFT) data, performing molecular dynamics (MD) simulations, to active learning and property calculations. An alpha version is available (see below). Completion of version 1 is due April 2025.
● Automates development of potentials requiring only the material and temperature range as input
● Generates graphs/figures/tables of phonons, optimized geometry, elastic constants, rdfs at potential- and DFT-level.
● RF-MEAM and machine-learning moment tensor potentials supported
● Fully automates setup and analysis of jobs and scheduling and monitoring of all tasks
● Interfaces with CASTEP/VASP, MEAMfit/MLIP2 and LAMMPS
● Uses active-learning (query by committee and D-optimality criterion supported) to automate training-set construction
TRAINING INFORMATION
STFC does not currently provide training for this software.
ACCESS
This software is available via GitLab.
castep_outputs – provides standard interface for using CASTEP
CAPABILITIES
The castep_outputs software can parse CASTEP output files to a Python dictionary. It provides standard interface for using CASTEP, a platform for developing and using Python post-processing tools on CASTEP data, and a centrally supported standard parser for difficult to machine-parse files and processes it into a standard format.
TRAINING INFORMATION
STFC does not currently provide training for this software.
ACCESS
ChemShell – provides a suite of advanced modelling methods for scriptable computational chemistry environments
CAPABILITIES
ChemShell is a scriptable computational chemistry environment. It provides a suite of advanced modelling methods and is designed to scale – from simple workflows to massively parallel calculations on supercomputers.
TRAINING INFORMATION
Training resources are available here.
There are also several training events supported by CoSeC.
ACCESS
This software is open-source and available here.
DL Visualize – provides an integrated environment for data visualization and analysis
CAPABILITIES
DL Visualize is designed to provide an integrated environment for data visualization and analysis. It supports the creation and visualization of molecules and atomic structures in two or three dimensions and can display calculated results as graphs, contours and isosurfaces.
TRAINING INFORMATION
STFC does not currently provide training for this software. Please contact Dr Barry Searle for further information.
ACCESS
This software is available via GitLab
DL_ANALYSER – a utility software tool to carry out post analysis of simulation trajectories produced from DL_POLY simulation package
CAPABILITIES
DL_ANALYSER is a utility software tool to carry out post analysis of simulation trajectories produced from DL_POLY simulation package. It can identify, quantify and carry out statistical analysis of various modes of atomic interaction.
TRAINING INFORMATION
Online training materials for DL_ANALYSER are available at DL_Software Digital Guide (DL_SDG). See here for more information.
ACCESS
This software is free via STFC licence for non-commercial, academic use. Commercial licence can be purchased via SCD’s BID.
dl_excurv – provides EXAFS analysis code developed for the UK’s Synchrotron Radiation Source
CAPABILITIES
dl_excurv provides EXAFS analysis code developed for the UK’s Synchrotron Radiation Source. It can use potential for functional groups rather than requiring all atoms to be modelled, and can producing details of the local atomic environment with EXAFS fitting based on simple atomic potentials.
TRAINING INFORMATION
STFC does not currently provide training for this software. Please contact Dr Barry Searle for further information.
ACCESS
This software is available via GitLab
DL_FIELD – a utility software used to setup force field models for running molecular dynamics simulations using DL_POLY
CAPABILITIES
DL_FIEL is a utility software used to setup force field models for running molecular dynamics simulations using DL_POLY. It contains a wide range of force field schemes that can be used to set up a variety of system models including biological, general organic molecules and inorganic materials.
TRAINING INFORMATION
Online training for DL_FIELD is available via the DL_Software Digital Guide (DL_SDG). See here for more information.
ACCESS
This software is available for non-commercial, academic use here.
A commercial licence can be purchased via SCD’s BID.
DL_MESO – a general purpose mesoscale simulation package for modelling different fluid and soft matter systems at larger than atomic length and time scales
CAPABILITIES
DL_MESO is a general-purpose mesoscale simulation package capable of modelling many different fluid and soft matter systems at larger than atomic length and time scales. It consists of highly scalable Lattice Boltzmann Equation (LBE) and Dissipative Particle (DPD) codes.
TRAINING INFORMATION
Tutorials and practical exercises in using DL_MESO are available in the DL_Software Digital Guide. See here for more information.
ACCESS
This software is available via academic licence here.
A licence for commercial use can be purchased via annual subscription by contacting Michael Seaton.
DL_POLY – a general purpose classical particle dynamics simulation package
CAPABILITIES
DL_POLY is a general purpose, classical particle dynamics simulation package. It provides a wealth of integration algorithms and functionality for modellers from diverse communities.
Developed under the auspices of EPSRC and NERC through community supported funded schemes such as CoSeC’s CCP5 and HEC-MCC, DL_POLY is free and open source software available to download from GitLab with a free user community access via email-list registration.
TRAINING INFORMATION
Training for DL_POLY is available via CoSeC.
Online training materials are also available at DL_Software Digital Guide (DL_SDG). See here for more information.
ACCESS
To access DI_POLY, register here.
DL-FIND – is a geometry optimisation library designed for atomistic simulation codes
CAPABILITIES
DL-FIND is a geometry optimisation library designed for atomistic simulation codes. It provides methods for local minimisation, transition state search, reaction path optimisation, conical intersection optimisation and population-based optimisation.
TRAINING INFORMATION
Online tutorials and training for DL-FIND are provided via the ChemShell computational chemistry environment.
ACCESS
This software is open-source and available here.
dlpoly-py – a python framework around DL_POLY code
CAPABILITIES
dlpoly-py is a python framework around DL_POLY. It is compatible with modern versions of DLPOLY 5.0, and offers the possibility of building complex reproducible workflows or usage of DL_POLY from modern environments as jupyter notebooks.
TRAINING INFORMATION
Informal training is available via DL_POLY hacks.
ACCESS
This software is available under the terms of the BSD 3-Clause license and can be accessed via GitLab, pypi and conda.
Janus-core – a python framework that integrates various machine learnt interatomic potential of current generation, MACE, M3GNET and CHGNET, Sevennet and Nequip
CAPABILITIES
Janus-core is a python framework that integrates various machine learnt interatomic potential of current generation, MACE, M3GNET and CHGNET, Sevennet and Nequip. It provides an easy entry point to learn MLIP for materials simulations, providing workflows to achieve complex tasks in modelling together with training and fine-tuning machine learnt potentials.
TRAINING INFORMATION
STFC provides online tutorials, that can be run via google colab, or on your machine. Code has been used at CCP5 Summer School advanced courses too. Do not hesitate to contact the team via github issues if you need help.
ACCESS
This software is open-source and available via GitHub and PyPI.
Muon Spectroscopy Computational Project – develops software and methods to help experimental scientists to understand and better interpret their results with the help of state-of-the-art computational techniques
CAPABILITIES
The Muon Spectroscopy Computational project develops software and methods to help experimental scientists to understand and better interpret their results with the help of state-of-the-art computational techniques.
TRAINING INFORMATION
Available training includes the tool documentation on MSCP webpage.
A tutorial for pymuon-suite is also available via the Galaxy Training Network. See here for more information.
ACCESS
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AbINS – a tool for simulation of vibrational spectroscopy with neutrons, provided as a plug-in within the Mantid framework
CAPABILITIES
AbINS is a tool for simulation of vibrational spectroscopy with neutrons, provided as a plug-in within the Mantid framework. It can import phonon data from a range of other packages and works to account for limitations of real-work inelastic neutron scattering instruments. Python scripting is also available for more advanced users.
TRAINING INFORMATION
ISIS Neutron and Muon regularly run general training schools, which include an AbINS tutorial.
ACCESS
This software is available via the Mantid Project.
CASINO – calculates material properties using an explicit description of electron-electron correlation via Quantum Monte-Carlo (QMC) methods
CAPABILITIES
CASINO calculates material properties using an explicit description of electron-electron correlation via Quantum Monte-Carlo (QMC) methods. This addresses the many-body problem directly, without using the uncontrolled approximations of Density Functional Theory.
TRAINING INFORMATION
STFC does not currently provide training for this software.
ACCESS
This software is available via online application for academic research. See here for details
CASTEP – a leading code for calculating the properties of materials from first principles
CAPABILITIES
CASTEP is a leading code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of materials proprieties including energetics, vibrational properties and spectroscopic features.
TRAINING INFORMATION
The CASTEP developers group regularly organise week-long residential workshops for both beginners and experienced users. See here for more information. A half-day course on DFT using CASTEP for Neutron Science is also available at ISIS Neutron Training Course
ACCESS
This software is available for non-commercial users here.
Prospective commercial users can obtain CASTEP through the BIOVIA Materials Studio product.
CRYSTAL – a general purpose program for the study of the electronic structure of periodic systems
CAPABILITIES
CRYSTAL is a general-purpose program for the study of the electronic structure of periodic systems. It employs a Gaussian basis set and provides a wide range of features including automated geometry editing, hamiltonians and periodic systems.
TRAINING INFORMATION
STFC does not currently provide training for this software.
Several tutorials are available at Crystal Tutorial Project.
ACCESS
This software is available to purchase here.
Academic users in the UK may access this software for free here.
ELK – an all electron electronic structure code capable of simulating the properties and dynamics of condensed matter
CAPABILITIES
ELK is an all-electron electronic structure code, capable of simulating the properties and dynamics of condensed matter. It uses a full-potential linearised augmented-plane wave (LAPW) basis set with fully non-collinear 2-component spinors.
TRAINING INFORMATION
STFC does not currently provide training for this software. Documentation is availalbe at The Elk Code.
ACCESS
This software is open– source and available here.
Euphonic – a Python library for interpolation of phonon data and computation of coherent neutron scattering spectra
CAPABILITIES
Euphonic is a Python library for interpolation of phonon data and computation of coherent neutron scattering spectra. It includes some useful command-line tools for analysis of phonon data and simulation of powder-averaged spectra.
TRAINING INFORMATION
ISIS Neutron and Muon regularly run general training schools which can include tutorials for Euphonic.
ACCESS
This software is open-source and available here.
ONETEP – a linear scaling code for quantum mechanical calculations based on density functional theory
CAPABILITIES
Order-N Electronic Total Energy Package (ONETEP) is a linear-scaling code for quantum-mechanical calculations based on density-functional theory (DFT). Its capabilities are wide ranging, including numerous DFT functionals, pseudopotentials, electronic analysis and more.
TRAINING INFORMATION
Training is available via the ONETEP Developer’s group. See here for more information.
ACCESS
This software is available free of charge for academic use.
Prospective commercial users can obtain ONETEP from BIOVIA. See here for more information.
QUESTAAL – an advanced electronic structure code featuring a powerful many-body perturbation theory implementation
CAPABILITIES
QUESTAAL is an advanced electronic structure code featuring a powerful many-body perturbation theory implementation. It allows for accurate treatment of electronic correlation in a wide range of materials. Various material properties including charge and spin response functions can also be calculated with high accuracy and precision.
TRAINING INFORMATION
To access training information on how to use QUESTAAL, please access the documentation.
ACCESS
QUESTAAL is open-source software, available via the following link: Getting Questaal.
Wannier90 – a special localised representation of the electronic structure of solids to facilitate the calculation of a wide range of material properties
CAPABILITIES
Wannier90 provides a special localised representation of the electronic structure of solids that can be used to facilitate the calculation of a wide range of material properties.
It provides detailed analysis of electronic structure properties in materials, clear identification of physically significant features, and an efficient numerical method for evaluating complex quantities.
TRAINING INFORMATION
Training for this software can be accessed through Support-Wannier90.
ACCESS
For access to this software with download and installation instructions: Wannier90.
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