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What’s New in MedeA® Version 2.20

MedeA 2.20 provides a wide range of enhancements and new capabilities in the MedeA® environment.

MedeA-HT-Launchpad accelerates high throughput calculations. MedeA-HT-Launchpad provides tools to create compendiums of systems and configurations (structure lists) from InfoMaticA databases and VASP trajectories, tools to build combinatorial libraries, tools to store structures and results of high throughput calculations, and utilites for sorting and duplicate removal.

MedeA-UNCLE has been updated to the latest release from the groups of Gus Hart at Brigham Young University and Stefan Müller at Hamburg University of Technology, enabling robust and automatic optimization of cluster expansions by means of state-of-the-art algorithms.

The Amorphous Materials Builder has been extensively enhanced to support the addition of amorphous phases to existing structures, additional options for rigid and semi-rigid systems, and the construction of layered models; the layer builder can be used to build bi-layer systems.

Extensive enhancements to the MedeA® environment have been undertaken including updates to symmetry related functionality, improved reporting in MedeA-Flowchart output for structure list based calculations, improved windows handling on Windows and Linux, extensions to interactive help and documentation, enhanced docking capabilities, and improved property handling for MedeA-Flowcharts. Calculations applying an implicit solvation model (VASPsol) are supported in all VASP-based modules.

Forcefields within the MedeA® environment are actively maintained, developed, and validated; parameters for several chemical groups have been refined in this release as summarized below.

MedeA 2.20 New Capabilities

MedeA-Amorphous-Materials-Builder

  • New options for extending existing models - e.g. for stepwise assembly of solvated systems
  • Simplified construction of systems such as partially ordered surfactant monolayers and lipid bilayers
  • Improved handling of fused ring structures in cage structures and extended polycyclic materials such as kerogens and asphaltenes
  • Added control of flexibility of individual component molecules during building
  • Substantial performance enhancements

MedeA-HT-Launchpad:

  • Provides support for high throughput calculations with foreach structure, structure list, and subsitutional building tools
  • Enhanced structure list creation and management
  • Flexible substitutional structure building capabilities

MedeA-Phonon:

  • Phonon calculations are now accessible in MedeA-Flowcharts permitting their use
  • in high throughput investigations
  • Phonon can now employ VASP, MOPAC, and LAMMPS to perform vibrational calculations

MedeA-Gaussian:

  • The default Gaussian DFT calculation functional is now B3LYP
  • Enhancements have been made to the display of orbitals and densities

MedeA-VASP:

  • Isothermal-isobaric ensembles (nPT) enabled for ab-initio molecular dynamics simulations
  • Support for molecular dynamics calculations in MedeA-VASP Flowcharts
  • The implicit solvation model (VASPsol) is now supported for all VASP-based simulations (including Transition State Search and Phonon)
  • The latest VASPsol release has been incorporated, allowing non-collinear calculations, for example
  • Enhanced potential reports in VASP calculations
  • The system charge state can now be set in MedeA-VASP Flowcharts
  • The number of bands can be easily controlled in MedeA-VASP Flowcharts

MedeA-Flowcharts:

  • Support for simple minimization and dynamics in flowcharts has been incorporated

MedeA-Forcefields 

  • PCFF+:
    • Refined parameters for cyclopropane, cyclopentane, and related compounds
    • Refined bond, nonbond, and torsional parameters, and bond increments for silanols
    • Templates for fused ring aromatic systems have been enhanced
    • Enhanced template rules for aromatic nitrogens
    • Refined parameters for sulfone groups
    • Improved charges and nonbond parameters for thiols and sulfides
  • Mie:
    • Support for Mie potential form for LAMMPS
  • Comb3:
    • Support for the SiO2 comb3 forcefield developed by France-Lanord and Wimmer
  • Trappe:
    • Additional parameters for thiols and sulfides
  • AUA and AUA+:
    • Additional parameters for amines and alkanolamines (AUA)
    • Extensions of parameters for branched esters (AUA+)

MedeA-GIBBS:

  • Additional library entries for hydrocarbons (AUA description)
  • Extension of the use of swap and exchange moves to molecules
  • Enhanced molecule placement for branched molecules
  • Extension of the use of variables for handling initialization of single phase simulations in MedeA-GIBBS Flowcharts

MedeA-Infrastructure and Builders:

  • Enhanced temporary directory handling for Windows
  • A flexible query based dialog is now employed for previous structure, analysis, and flowchart retrieval from the JobServer
  • Improved handling of accelerator keys for mouse actions
  • MedeA® now includes functionality to upload local directories and calculation results to the NoMaD repository.

MedeA-JobServer and MedeA-TaskServer:

 

  • A number of security upgrades have been made to the JobServer and TaskServer
  • Multiple JobServers can now use a single TaskServer

Platform Support:

MedeA 2.20 is supported on 64 bit Windows and 64 bit Linux operating systems.

Publish while: 
2016 Jul 4 - 01 - 2016 Oct 23 - 23

News & Views

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