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  • Katherine Hollingsworth

MedeA Software Release MedeA 3.8 -- Micro to Macro!



Materials Design Announces the Release of MedeA 3.8 “Micro to Macro”!

Materials Design is delighted to announce the latest release of its world-leading materials simulation MedeA Environment. The MedeA 3.8 release features a wide range of enhancements: from machine learning and materials informatics to microstructure construction tools and the latest innovations in density functional theory.


Dr. Erich Wimmer, Chief Scientific Officer and Chairman of the Board at Materials Design, said of the new MedeA release:

In the context of Materials Design’s machine learning offering, MedeA 3.8 provides access to VASP 6.4.2, extensive access to VASP's machine-learning force field (MLFF) capabilities (which takes ab initio molecular dynamics calculations to the next level) together with many additional enhancements. We are particularly excited to announce the availability of the "Polymer Expert" de novo design module in MedeA 3.8.


MedeA Polymer Expert was developed in collaboration with Dr Jozef Bicerano, the author of the well-known P3C polymer property method. It allows you to find materials with desired properties in a repeat unit space containing well over one million entries. As integrated into the MedeA Environment, the Polymer Expert is extremely efficient and intuitive.


A list of major enhancements in the MedeA 3.8 release is provided below.


Dr. Wimmer added, "It has been a delight to see the development of MedeA over the years, and MedeA 3.8 is particularly satisfying to me. We have extended and enhanced many capabilities that Materials Design provides access to. These are cutting-edge methodologies developed by the world's leading researchers, empowering customers to achieve diverse objectives in materials science. We serve chemists, physicists, engineers, and materials scientists who are discovering bio-derivable polymers, improving batteries, optimizing processes and energy sources, and obtaining a host of materials insights along the way. Our customers consistently express their enthusiasm for the productivity the MedeA Environment offers and the scientific support the entire Materials Design team provides.”


About the MedeA Atomistic Modeling and Simulation Environment


Scientists and engineers in industry, academia, and research institutions employ the MedeA Environment to simulate materials properties and understand diverse phenomena. The MedeA Environment enables users to create better products by accurately simulating materials properties and understanding key mechanisms.

The MedeA Environment integrates world-leading structural databases (totalling over one million entries), electronic structure programs (VASP, GAUSSIAN, MOPAC), molecular dynamics (LAMMPS), and Monte Carlo methods (GIBBS) and a host of powerful building, editing, and analysis tools in a unified infrastructure allowing the creation of efficient workflows. Its innovative high-throughput (HT) capabilities enable the exploitation of computational resources to explore complex design spaces.


About Materials Design


Materials Design serves users in academia, government laboratories, and industrial enterprises worldwide. Materials Design develops the MedeA software environment for electronic structure analysis, atomistic and mesoscale simulation, and materials property data handling and offers contract research and development, software user training, and scientific consulting services. From energy and transportation to chemistry, microelectronics, clean-tech, and aerospace, Materials Design serves customers who have a wide range of interests and materials challenges.

 

MedeA 3.8 December 2023

Description of MedeA  3.8 New Features and Enhancements  

1. Builders and Editors:

  • Microstructure Builder (New)

The MedeA Microstructure Builder creates microstructure models for atomistic simulations using a Seed & Growth algorithm with starting points either placed randomly or at user-specified coordinates within a supercell. Each such point is used as an origin to grow a crystalline grain by adding atoms from that seed point outwards until a grain boundary is encountered.

The models created by the MedeA Microstructure Builder can be used with other MedeA tools to explore microcrystalline materials' structural, energetic, and dynamic characteristics.

  • Enhancements for exporting structures to extxyz

  • Enhancements for bond computation

  • Enhancements for assigning element colors

  • Addition of the ability to use a variable for density in the amorphous builder stage

  • Added an automated orthorhombic construction mode to the Supercell Builder

2. Engines:

  • VASP:

    • Update to latest VASP 6.4.2 executables for Linux and Windows

    • All combinations of constraints for atom positions, cell volume and shape are enabled for structure optimization

    • Added user interface support for many molecular dynamics features through (thermostats, constraints, monitoring)

    • Added support for isoenthalpic isobaric (nPH) ensemble

    • Added ability to refit machine-learned forcefields

    • New user interface for fine-tuning and optimizing the process for on-the-fly machine learning and refitting of forcefields.

    • Faster loading of machine-learned forcefields

  • LAMMPS:

    • Update of automatically produced plots (post-processing)

    • Addition of an option for writing a trajectory in native LAMMPS format

    • Addition of warning if there are frozen atoms during an NPT run

  • GIBBS:

    • GIBBS 9.7.8 executables for Linux and Windows


  • GAUSSIAN:

    • Optimization of transition states accessible in flowcharts


3. Forcefields:

  • MLPG:

    • Enhancement to allow for manual assignment of structures to training/validation sets

    • Addition of "Coordinates" property when importing into the Fitting Data Manager


  • Enhancements on forcefields handing in FFO

  • PCFF+:

    • Refined nonbond parameters for carbon in acetal groups

4. Property modules:

  • Polymer Expert (New)

The Polymer Expert is a new module in the MedeA Environment in MedeA 3.8. The innovative Polymer Expert capability facilitates de novo polymer design through high-efficiency access to a substantial (>1.1 million entries) database of polymer properties, PEARL (Polymer Expert Analog Repeat unit Library). Polymer Expert allows you to identify novel polymers by querying the PEARL database based on properties and property ranges. You can also search for biologically derivable analogs within the PEARL database. Polymer Expert was developed in collaboration with Jozef Bicerano, the author of Prediction of Polymer Properties, Marcel Dekker, Inc. (2002) and is described in the paper: J. Bicerano, D. Rigby, C. Freeman, B. Leblanc, and J. Aubry, Polymer Expert - A Software Tool for De Novo Polymer Design, 2023 (submitted for publication).

  • P3C:

In consultation with Jozef Bicerano, various upgrades to P3C have been made, extending and adding correlations, allowing MedeA P3C to report polymer properties for larger systems and presenting results to users in an improved and more intuitive manner.

  • Deposition:

    • Enhancements for subsets used in deposition


  • MT:

    • Faster loading of machine-learned forcefields

    • Output enhancements

5. Analysis:

  • Enhancement for pair correlation panel

6. Infrastructure:

  • Addition of the MedeA Python environment

  • Update of IntelMPI to the 2019 version on Linux






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