Software
Click on the text below to learn more about obtaining each software.
RASPA: Molecular Simulation Software for Adsorption and Diffusion in Flexible Nanoporous Materials
RASPA is a software package written in C for simulating adsorption and diffusion of molecules in flexible nanoporous materials. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo in various ensembles including symplectic/measure-preserving integrators, Ewald summation, Configurational-Bias Monte Carlo, Continuous Fractional Component Monte Carlo, Reactive Monte Carlo, and Baker’s minimization. Applications of RASPA include computing coexistence properties, adsorption isotherms for single and multiple components, self- and collective diffusivities, reaction systems, and visualization.
Partial Atomic Charges in Metal-Organic Frameworks (PACMOF) from Machine Learning
PACMOF is a small and easy to use python library that uses machine learning to quickly estimate partial atomic charges in metal-organic frameworks. The pre-trained Random Forest model (Scikit-learn) in PACMOF generates high-quality charges of the same accuracy as that of Density Derived Electrostatic and Chemical (DDEC), but without needing hours of periodic-DFT calculations. PACMOF is made with high-throughput screening in mind, where you can get charges on a large number of CIF files in parallel, using a Dask backend with options to write the output charges into new CIF files, and to use user-trained machine learning models instead of the pre-trained one (compiled during installation).
Music – Multipurpose Simulation Code
Music is our older Fortran90 MUltipurpose SImulation Code. Music can be used for simulation of diffusion and adsorption in porous materials, liquid and gas simulations, and may be easily extended for solid simulations. It includes such forcefield elements as 12-6 Lennard-Jones and Buckingham potentials. Coulombic interactions are handled with Ewald summations and also smooth cutoff schemes. Molecules may be fully flexible, including bond vibration, bond angles, bond torsion, and intramolecular repulsion. Another strong point of Music is that it can combine MD and MC simulations easily to create hybrid sampling schemes (e.g., Hybrid Monte Carlo).
MOFid
The goal of this software is to assign machine-readable MOF identifiers using an automated cheminformatics algorithm. MOFid and the related MOFkey provide detailed information of a MOF’s composition, metal nodes, linkers (via SMILES), and topology in a format that is useful for data mining. It is available as a web interface or downloadable C++/Python code.
ToBaCCo 1.0
ToBaCCO is a python package that constructs MOFs on the basis of user-provided metal nodes, nodular organic building blocks, connecting building blocks, and topologies.
PSA
PSA is an open-source MATLAB code for simulation of pressure-swing adsorption processes based on continuum mass, energy, and momentum balance equations coupled with the linear driving force model and an adsorption isotherm model.