![]() For porous structures, like zeolites and MOFs, sometimes it is more useful to visualise the pores of the structures, rather than the atoms. Examples of materials are metals, metal-oxides, ceramics, biomaterials, zeolites, clays and metal-organic frameworks (MOFs). Here, we present a visualisation package aimed at material science. The human brain does not like tables of data, it likes graphs and plots, and from these we visually observe trends, patterns, relationships and exceptions. That is the job of ‘molecular visualizers’: to transform the data for efficient perception by the human brain. Staring at the atomic positions in a CIF- or PDB-file for a long time will not get you closer to understanding the molecular structure. Visualisation is another crucial tool for obtaining molecular level insight. In this paper we present the second part, iRASPA, a macOS visualisation app for material scientists. This software packages is well suited for simulating adsorption and diffusion of molecules in flexible nanoporous materials and to obtain molecular level information on these systems. Recently, we have made our advanced Monte Carlo code called ‘RASPA’ open source. Simulation methodology is not only to make simulations more efficient, but rather it usually provides additional information that is hard to obtain otherwise. For example, using transition state theory for rare events, the reaction coordinate provides valuable information what exactly happens during the transition and why it occurs. Therefore, even if you could atomically simulate the system on large space and time-scales, in many cases it is preferable to simplify the system significantly to focus on one particular aspect. To really get to the bottom of the physical, chemical and biological phenomena that occur, it is vital to elucidate the what, why and hows. However, while the increase in computational power and algorithms enable simulation of larger systems that can be run for longer times, one simulation itself is just one typical reproduction of the physics. Density Functional Theory (DFT) is currently applicable to hundreds of atoms, but using a classical formulation trillions of atoms can be used. Molecular simulation is a powerful tool to conduct ‘in-silico’ experiments on atomic systems. The software is freely available from the Mac App Store. Leveraging the latest graphics technologies like Metal, iRASPA can render hundreds of thousands of atoms (including ambient occlusion) with stunning performance. Main features of iRASPA are: structure creation and editing, pictures and movies, ambient occlusion and high-dynamic range rendering, collage of structures, (transparent) adsorption surfaces, cell replicas and supercells, symmetry operations like space group and primitive cell detection, screening of structures using user-defined predicates, and GPU-computation of helium void fraction and surface areas in a matter of seconds. Each project contains a scene of one or more structures that can initially be read from CIF, PDB or XYZ-files, or made from scratch. A document contains a gallery of projects that show off the main features, a CloudKit-based access to the CoRE MOF database (approximately 8000 structures), and local projects of the user. The latter allows collaboration on a shared document (on High Sierra). iRASPA is a document-based app that manages multiple documents with each document containing a unique set of data that is stored in a file located either in the application sandbox or in iCloud drive. A new macOS software package, iRASPA, for visualisation and editing of materials is presented.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |