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Software Releases

Materials Design offers our diverse clients the tools they need to stay at the top of their respective fields. MedeA is a leading atomistic simulation software package that brings together what you need in a user-friendly environment. 

 

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Software Releases

MedeA  3.7    April 2023  

 

Description of MedeA  3.7 New Features and Enhancements  

 

The MedeA 3.7.0 release provides new capabilities for vibrational analysis based on molecular dynamics trajectories, updated VASP executables (6.4.1) with full integrated MedeA support, extensive enhancements in Machine Learning based simulation, and a broad array of general improvements to the entire MedeA environment.

An overview of updates in this MedeA release is provided below.

  1. Builders and Editors:

    • Subsets:

      • Additional capability to select complete molecules through the "extend selection" option

      • Targeted performance enhancements for large number of atoms

      • Enhancements for editing subset coloring

      • Enhancements for subset splitting capabilities

      • Enhancement in the Subset Overview panel

      • Addition of an elements option to the attach fragments functionality

      • Thermosets:

        • Enhancements for controlling the conversion extent

      • Enhancements for import of structures in extended xyz format

      • Enhancements for import of large PDB structures

      • Gnuplot update (5.4.6)

      • New functionality for the deletion of overlapping atoms in a defined selection

      • Enhancements in handling of mesoscale structures in the supercell builder

      • Enhancements for Interface builder

      • Three additional popular atom color schemes added
         

  2. Engines:

    • VASP:

      • VASP 6.4.1 executables with integrated MedeA support (NEW)

      • Site-specific output of NMR chemical shift data

      • Addition of chemical shift data and magnetic susceptibility to the workspace

      • Enhancements for output of EFG, Hyperfine parameters, and Born effective charges

      • Upgraded POSCAR files containing elements and atom-site correspondence

      • Return status given in structure lists and trajectories, enabling easy convergence assessment for large datasets

      • MLFF enhancements:

        • Enabling MLFF-based forces in trajectories

        • Creation of a separate MLFF_TrainingSet.sli structure list with significant, ab initio-calculated structures/data (e.g. for further use in machine-learning applications and forcefield fitting)

        • Addition of Bayesian Error and RMSE Analysis in graphical form for VASP-MLFF

        • Reduced MLFF OUTCAR data volume via trajectory file frequency for swift post-processing and trajectory creation

    • LAMMPS:

      • LAMMPS 2Jun2022 executables (NEW)

      • Automatic selection of correct executable for extended GPU support

      • Addition of Nose-Hoover-Andersen in list of control temperatures in LAMMPS NVT/NPT stages

      • Enhancements form minimization stage under pressure

      • Enhancements for restoration of United-Atom hydrogens for carbon atoms of unsaturated hydrocarbons

    • GIBBS:

      • Several updates/enhancements to GIBBS trajectories and generated structure lists

      • Enhancement in improper torsions’ input

      • Extensions for handling and reporting of 1-2/1-3/1-4 interactions in GIBBS

    • MOPAC:

      • Enhancement for calculating thermodynamic properties for a single temperature in a Thermodynamics stage   
         

  3. Forcefields:

    • MLPs & MLPG:

      • Support for ACE MLPs (in LAMMPS, CPU & GPU) (NEW)

      • Full user control of hyper-parameter convergence tolerance

      • Checking and recording of status for VASP calculations

      • Enhancements on data handling

      • Extensions for tabulated forcefields

    • PCFF+:

      • Introduction of unique atom types for inorganic sulfate anions
         

  4. Property modules:

    • P3C:

      • Refined 5 membered rigid rings recognition and contribution in P3C in consultation with Dr. Jozef Bicerano

      • Updated P3C tab in Molecular Builder for repeat units containing over 100 atoms, allowing application of P3C computation on demand

      • Enhanced handling of repeat units with common head and tail atoms

      • Enhanced handling of silane based repeat units

    • Electronics:

      • Calculation and graphical presentation of carrier mobility (NEW)

    • PhononMD: (NEW)

      • Vibrational density of states and its partial contributions from molecular dynamics velocity autocorrelation functions

      • Automated plot creation facilitating analysis of results

      • Vibrational thermodynamic properties such as internal energy, entropy, Helmholtz free energy, and heat capacity
         

  5. Citations/References:

    • New link in "Help" menu in MedeA that points to the "How to cite" section in the MedeA manual

    • Downloadable ris/bibtex references for MedeA and MedeA tools/modules
       

  6. JobServer & TaskServer:

    • Enhancements for downloading structures from the JS containing spaces in their names

    • Addition of warnings if GPU requested but not present on the TaskServer

    • New capability for automated zip file creation and download

 

 

 

MedeA  3.6    December 2022  

Description of MedeA  3.6  New Features and Enhancements  

 

1. Engines:

  • VASP:

    • Updated VASP executables to version 6.3.2

    • Full support for reuse of machine-learned forcefields (MLFF) obtained from previous molecular dynamics simulations for other VASP calculations and MedeA modules

    • Using the VASP GUI, reuse of MLFF descriptions are enabled for:

      • Single point calculations

      • Structure optimizations

      • Molecular dynamics simulations

      • Electron-phonon coupling

      • MT - Elastic properties

      • Property computations added for zone center phonons, work functions, and formation energies

    • Furthermore, reuse of MLFF descriptions are supported for modules such as

      • MedeA Phonon

      • MedeA MT

      • MedeA TSS

      • MedeA UNCLE

    • Enhanced reporting of calculation parameters for meta-GGA functionals

    • Updated entry field descriptions

    • Restore from previous job completed by PAW options control

    • Updated user interface handling for L(S)DA+U parameters

    • Additional SCF algorithm options supported for SCAN-rvv10

  • LAMMPS:

    • Support for LAMMPS set cell stage remapping of atomic coordinates

    • Cohesive energy density stage enhanced for certain forcefields

    • Enhanced trajectory structure naming

  • GIBBS:

    • Enhanced handling of phase composition in the MedeA interface

  • GAUSSIAN:

    • IR and Raman spectra reports have been enhanced

 

2. Property Modules:

 

  • Phonon:

    • Support reuse of machine-learned forcefields from VASP (MLFF) for evaluating

          all vibrational properties, such as phonon dispersion and energy density of states,
          thermodynamic functions, and non-electronic contributions to IR and Raman spectra

  •  MT:

    • Support for reuse of machine-learned forcefields from VASP (MLFF) to obtain

          elastic, mechanical and thermodynamic properties

  • TSS:

    • Supports reuse of machine-learned forcefields from VASP (MLFF) to find

          transition states

  • Electronics:

    •  Re-enabled effective mass calculation from a previous VASP charge density task

  • UNCLE:

    • ​Supports reuse of machine-learned forcefields from VASP (MLFF) for exploring configuration space

    • Improved handling of the user interface in absence of an active structure

  • ​InfoMaticA:

    • ​Updated reporting of query result properties

  • Morphology:

    • ​Enhanced linkage to surface builder

3. Flowcharts:

  • Enhanced deformation optimization options for LAMMPS and VASP

  • Optimized automated Job title handling

  • Improved user interface support for keyboard short cuts

  • Enhanced handling of flowchart description editing

  • Compress layer stage enhancements

  • General user interface enhancements

  • New Surface Builder stage

 

4. Builders and Editors:

  • Updated Builders & Editors:

    • Extensive general user interface enhancements and updates

    • Enhanced support for 4-coordinate pyramidal atoms

    • General usability enhancements

    • Substantial subset management enhancements

  • Thermoset Builder:

    • Enhancements for multisite systems and reaction probability support

  • Amorphous Materials Builder:

    • Updated handling of input systems with active bonds

    • Improved handling of incorrectly bonded input systems

  • Surface Builder:

    • Enhanced control of angular positioning

  • Mesoscale:

    • Enhanced handling of the homepath variable on Windows

 

5. Forcefields:

 

  • PCFF+:

    • Accurate parameters for battery electrolyte systems including organic carbonates

  • MLPG:

    • MLPG post-processing enhanced for NNP

    • MLPG enhanced SNAP hyperparameter optimization

    • Updated delta learning training set support

    • Enhanced SNAP .frc file description support

  • ForceField Optimizer (FFO):

    • Enhanced reporting for spin polarized training set systems

    • Enhanced handling of validation set conditions

  • MEAM:

    • Improved support for custom MEAM forcefields

  • General:

    • Support for tabulated forcefields in LAMMPS

 

6. Analysis Tools:

   

  • Enhanced band structure plots for certain systems

  • Export Band Structures and Densities of States on Windows:

    • Enable combined plots for large datasets and systems

  • Export Phonon Dispersions and Densities of States on Windows:

    • Enable combined plots for large datasets and systems

  • Enhanced animations of phonon modes from phonon dispersion plots

  • Enhanced orbital view

 
7. Maintenance:

     

  • MD Maintenance: updated user interface for usability

 

8. JobServer & TaskServer:

     

  • Improved handling of inaccessible resources 
     

MedeA  3.5    June 2022  

 

Description of MedeA  3.5  New Features and Enhancements    

 
  

1. Flowcharts:  

  • A brand-new flowchart interface with improved ease of use for all flowchart stages 

  • Copy/paste functionality for all flowchart stages 

  • Ability to retrieve flowcharts from VASP runs submitted through the (non-flowchart) VASP interface 

  • A new Interfaces stage 

 

2. Builders and Editors:  

  • Structure Lists for calculation automation and information management are now available with the standard MedeA Environment 

  • Structure Lists can be directly created from several flowchart stages, such as:  '

    • VASP 

    • GIBBS 

    • Phonon 

    • MT 

    • TSS 

    • LAMMPS Deposition 

    • UNCLE 

  • Numerous enhancements for large PDB files  

    • Enhanced connectivity information handling 

    • Added ability to write large PDB files with hybrid36 extension (for systems containing 100,000 atoms or more) 

  • Added ability to read mmCIF files through OpenBabel 

  

2. Engines:  

  

  • VASP:  

    • Full VASP 6.3.1 support via MedeA 

    • On-the-fly machine-learned forcefields (MLFF): 

      • Accelerates ab initio molecular dynamics simulations employing machine learning, massively increasing accessible simulation times 

      • Creates a machine-learned forcefield using ab-initio molecular dynamics trajectories as training set as the simulation proceeds 

      • Continues machine-learned forcefield optimization running additional molecular dynamics simulations (for other systems) 

      • Applies machine-learned forcefield without further running ab-initio simulations 

    • Various improvements and optimizations for non-collinear VASP 6 and 5.4 calculations 

    • Enhanced of parsing efficiency of large OUTCAR files 

    • Further support of MetaGGAs (rSCAN, r2SCAN) 

    • Structure lists (ListOfResults.sli) with final structures and including calculated properties, suitable for forcefield fitting, are now created automatically further enhancing efficiency, analysis, and post-processing options 

 

  • LAMMPS:  

    • Updated to the 7Jan22 version  

    • Added support for new packages: 

      • PYTHON: both Linux and Windows, on CPUs and GPUs 

      • SPIN: both Linux and Windows, on CPUs and GPUs 

    • Improved GPU support: 

      • Support for Nvidia GPU cards with compute capabilities from 3.5 to 8.6 on both Linux and Windows 

      • Approximately 40% computation performance improvement for potentials using long-range Coulombic interactions  

    • Use new rigid pcff+ H2O model employing shake (which is now the default) providing superior rdf, and surface tension for water at ambient conditions  

   

3. Forcefields:  

  

  • PCFF+:  

    • Improved water model     

  

4. Property modules:  

  

  • Phonon:  

    • Structure list (DisplacedStructures.sli) created, suitable for forcefield fitting  

  • MT:  

    • Structure list (StrainedStructures.sli) created, suitable for forcefield fitting  

  • TSS:  

    • Structure list (EnergyProfileStructures.sli) created, suitable for forcefield fitting  

MedeA  3.4      December 2021  

Description of MedeA 3.4 

New Features and Enhancements   

 

1. Updated Builders & Editors 

 

  • Addition of controls on each system-view window 

  • Easy access to 3D viewing options through the controls on the system-view window 

  • Addition of visual aids / enhancements, such as: 

    • Depth cueing 

    • Control of perspective view 

    • Lighting options  

    • Creation of user-defined profile controlling 3D viewing options 

    • Axes and axes labels and positioning control 

  • Introduction of right panel with "switch" mode for access to multiple panels 

  • Replacement of a number of "floating windows" with right panel (e.g. edit cell/symmetry, supercell builder etc.) 

  • Update of "Docking" tool, including view of energies and ability of selection of any created configuration 

  • Geometric Analysis as a side-panel on the structure-view window (periodic systems) 

  • Several enhancements in the Trajectory animations, including: 

    • Increased rendering speed 

    • Improved efficiency in bond handling 

    • Improved control of viewing (mixed view) 

    • Animation panel on the trajectory animation window 

    • Smart access restriction to trajectories 

  • Structure Lists' animation, including plotting of properties and descriptors that are included / saved therein

 

2. Engines: 

 

  • VASP: 

    • Accelerated import for large OUTCAR files created by long molecular dynamics simulation

 

  • GIBBS:  

    • Calculation of sorption grids within the GCMC computation 

      • Accelerated grid construction 

      • Decrease of JS/TS traffic (streamlined grid transfer) 

      • Automated rebuild of grids if deleted or inappropriate 

      • Increased consistency (grid construction and simulation using a single set of binaries)

 

3. Forcefields: 

 

  • MLPG: 

    • Addition of neural network potentials by adding n2p2 to the MLPG 

    • Efficient inclusion of post-DFT approaches by using "Delta learning"  

    • Bond length, bond angle and torsion angle distribution analysis in the MLP data manager 

  

  • PCFF+: 

    • Refined parameters for trialkyl phosphates     

 

4. Property modules: 

 

  • Phonon: 

    • Enhanced analysis of Infrared and Raman spectra 

      • Specification of experimental conditions (polarized or unpolarized light / monocrystal or polycrystalline sample) 

      • Specification of incident and scattered light orientation and polarization orientation for Raman spectra 

      • Display of Raman cross section or Raman reduced spectra, handle the temperature (Bose) factor 

    • Enhanced analysis of thermodynamic functions 

      • Analysis of contributions of atoms in Cartesian directions to the thermodynamic functions 

      • Analysis of  thermal displacements of atoms as a function of temperature 

MedeA 3.3    June 2021

1. Builders and Editors:

  •  Edit cell

    • Added option to switch between standard cell orientation and a preset arbitrary orientation 

  • Supercell builder

    • Option to rotate to standard orientation (default) or to preserve orientation according to cell construction

  • Thermosets

    • Faster re-assignment of atom types (selective reassignment)

    • Increased the number of sites supported in multi-sites crosslinking

  • Subsets

    • Definition of subsets based on position criteria

    • Extensions on the ability to transfer subset information upon system editing (copy/paste, merge, create supercells etc)

    • Additional capability of freezing subsets via the Subset Manager stage

    • Calculation of bond orders along with bonds

    • Export to mol2 format for non-periodic and periodic systems

    • Enhancements to exporting to pdb format


2. Engines:

  • VASP

    • VASP 6.2.1 executables

    • Automated procedure to calculate accurate optical spectra including excitonic effects via the Time Evolution approach

    • Enhanced robustness of energy of formation and optical spectra simulations

  • LAMMPS

    • Updated to the LAMMPS29Oct20 official stable version

    • Supports NVIDIA GPUs on Windows

    • Supports running on OpenMP threads on Linux and Windows

    • Supports the PLUMED package on Linux

  • GIBBS

    • GIBBS 9.7.4

    • Improved handling of simulation output (configurations in pdb formats)

    • Extended use of variables as simulation input (ideal gas heat capacity)

    • Improvements on printed simulations' summary in Job.out


3. Forcefields:

  • MLP (Machine Learning Potentials)

    • Access to a variety of published machine learning potentials for use with MedeA LAMMPS

  • MLPG (Machine Learning Potential Generator)

    • Generation of machine learning potentials (on Linux and Windows)

  • Martini

    • Addition of recently published Martini 3 for CG simulations

  • ForceField Optimizer (FFO)

    • Enhanced support for fitting force and stress data

    • Enhanced support for triclinic cells

    • Improved performance for some forcefield classes


4. Property Modules:

  • Phonon and MT

    • Enable automatic evaluation of the energy of formation for the system by MedeA VASP 6, thus providing temperature dependent energy of formation, entropy and free energy of formation

  • TSS

    • Enable automatic evaluation of the energy of formation by MedeA VASP 6 for initial and final configuration, as well as for all optimized transition states

    • Various enhancements for performance

  • Electronics

    • Enable automatic evaluation of the energy of formation for the investigated system by MedeA VASP 6

  • P3C

    • Improvements in the calculation of 4 descriptors (Namide, Nco, Nhb, Nvkh) used in the calculation of Ecoh1 and Ecoh2

MedeA 3.2    7 December 2020

General

  • Improvements in structure 3D viewer:  

    • Line antialiasing for high quality cell and line draw views 

    • Updated perspective projection for depth perception  

  • Numerous documentation enhancements, updates, and new tutorials 

  • JobServer job imports have been enhanced 

  • Enhanced graph plot file export functionality 

  • Added property variables for use in Flowcharts 

  • Enhanced labelling


Databases

  • New MSI Phase Diagrams Database providing high-quality, evaluated phase diagrams, and related constitutional data  


Builders and Editors 

  • Thermosets:  

    • Support crosslinks between multiple types of site 

    • Optional user-controlled connection probabilities

  • Mesoscale: 

    • Perform mapping of a coarse-grained onto an atomistic system 

  • Nanoparticles:  

    • Improved algorithm, reducing particles build times for large systems


Engines

  • MedeA VASP:   

    • Automated calculation of energy of formation (VASP 6) 

    •  Excitonic effects in optical spectra from the model Bethe-Salpeter approach based on a model dielectric function 

    • Use of ScaLAPACK through the Advanced/Restart tab 

    • Listing of optical functions on a regular wavelengths grid in Job.out 

    • Optical functions output as variables in workspace for use in Flowcharts 

    • Addition of kinetic contribution to the average pressure obtained from molecular dynamics simulations

  • MedeA LAMMPS: 

    • Distribution analysis available in LAMMPS Analysis

    • Group analysis available in LAMMPS Analysis

    • Pair Correlation analysis available in LAMMPS Analysis

  • MedeA GIBBS: 

    • Enable the use of mesoscale forcefields (including MARTINI and SPICA)  

    • Enable the use of EAM forcefields - allowing simulation of e.g. hydride formation 

    • Use of 1-2/1-3/1-4 interactions as defined in the forcefield file (frc)

  • MedeA MOPAC:   

    • Updated version from Professor Jimmy Stewart


Property Modules  

  • MedeA QT:

    • New QT version: v1.2.31 on linux and v1.2.30 on windows 

    • Interactive correlation plot updates 

    • Residuals plot for all correlations 

    • All items on the Edit menu are disabled for the Models tab 

    • Green check marks and gray hint boxes are restored on column menus for the Training Set tab  

    • Plot menu items no longer appear on column menus for the Training Set tab 

    • Plot menu items are enabled only for "Model N" columns on the Models tab 

    • Additional logging capabilities have also been incorporated 

  • MedeA Phonon: 

    • Enable graphical display of thermodynamic functions, vibrational and electronic occupation contributions 

    • Updated support for valence forcefields with LAMMPS 

  • MedeA MT:  

    • Enable graphical display of thermodynamic functions

 

Forcefields 

  • PCFF+: Forcefield extensions based on validated analysis for:   

    • Extensions for ketones  

    • Enhanced atom typing rules for selected systems 

  • Added GAFF (General AMBER forcefield, for organic molecules) 

  • Added ReaxFF/CHONFClSi.frc 

  • Updated MEAM descriptions


Analysis Tools:  

  • New GUI for assembling and plotting thermodynamic functions (from Phonon and MT) 

  • Additional handling of trajectory animations 

  • Automated video creation for animations 

  • Fine control over frame selection for animations

 

 

MedeA 3.1    30 June 2020

 

MedeA 3.1 features: 
 

  • VASP 6 with a dedicated GUI 

  • mesoscale builder for creation of coarse-grained molecules 

  • Extensions to builders for handling coarse-grained systems (polymer builder, amorphous materials builder and thermoset builder)  

  • Flowchart support for mechanical modification of arbitrary systems through the Deformation module 

  • The direct simulation of emissivity 

  • The ability to start GIBBS Monte Carlo simulations from existing configurations 

  • Numerous PCFF+ forcefield enhancements 

  • Support for the latest version of LAMMPS 

  • A streamlined installation and administration interface 

  • The UNIFAC correlative simulation method  

  • A diverse array of high throughput simulation environment updates

  • Numerous enhancements throughout MedeA's infrastructure support the key themes of this release: accuracy and realism

 

Description of MedeA 3.1 new features and enhancements

 

Builders and Editors 

  • Mesoscale Builder: NEW builder for building coarse-grained molecules, using pre-defined beads or introducing new types of beads 

  • Polymer Builder: ability to build coarse-grained polymers 

  • Amorphous Builder: ability to build coarse-grained systems 

  • Thermoset Builder: ability to build coarse-grained thermosets 
     

Engines 

  • MedeA VASP  

    • VASP 5.4.4 and VASP 6.1.1 executables 

    • Dedicated VASP 6 GUI enabling easy access to newly implemented functionality of VASP 6.1.1 as listed below 

    • Space-time based approach for the calculation of polarizibility, providing essentially cubic rather than quartic scaling with system size, facilitating the study of larger systems

    • Accurate energy, forces and phonon modes from adiabatic connection applying the space-time algorithm (Low Scaling ACFDT/RPA) 

    • Automatic optimization of atom position on the ACFDT/RPA level of theory applying the space-time algorithm 

    • Accurate energy from Moeller-Plesset perturbation theory (MP2) 

    • Dielectric-dependent hybrid functionals (DDH/DSH) 

    • Electron-phonon interaction from full Monte-Carlo sampling of displacements or a single-configuration (Zacharias-Giustino approach) 

    • X-ray absorption spectroscopy (XAS)  

    • GUI access for applying electric fields 

    • Enhancements for NMR calculations

  • MedeA LAMMPS  

    • LAMMPS 3-March 2020 

    • Several enhancements on existing functionality 

    • Additional LAMMPS packages included in the build (LATTE, USER-COLVARS) 

    • Support for NVIDIA GPUs up to compute capabilities of 7.0 

  • MedeA GIBBS 

    • GIBBS 9.7.3 

    • Ability to start a single-phase simulation from a pre-built initial configuration 

    • Extended, and fully automated, Pivot move control

 

Property Modules  

  • Brand new Deformation Module to apply systematic stresses and strains to atomic models in a defined manner 

  • Molecular Descriptors: addition of new molecular descriptors facilitating correlative model creation

  • Brand new UNIFAC capability for vapor−liquid equilibria simulation based on correlations

 

Forcefields 

  • Extension of nonbond interactions in frc files to handle defined pair-interactions instead of using mixing rule (LAMMPS)  

  • New Mesoscale Forcefields:  

    • MARTINI  

    • SPICA  

  • pcff+ : Forcefield extensions for:  

    • Optimized parameters for Ba (based on BaCO3) 

    • New parameters for divalent Mg and Sr cations 

    • Improved parameterization of urea 

    • Extensions for -OCH3 terminated oligo-ethyleneglycols 

  • EAM

    • Combination of Morse Forcefield with Streitz-Mintmire charge equilibration  

  • TraPPE-UA+:  
     

Flowcharts:  

  • Subset Manager stage: providing the ability to create a subset in a flowchart 

  • Flowchart Library: several updates to existing flowcharts and addition of new flowcharts 
     

Analysis Tools:  

  • Optical Spectra:  

    • Display of blackbody radiation as a function of frequency 

    • Spectral emissivity 

    • Total emissivity as a function of temperature 

    • CIE 1931 and 1964 color spaces upon reflection and transmission, now both for spectral power distribution of Standard Illuminant D65 and of fluorescent lamp FL2 


MedeA's JobServer & TaskServer & Maintenance:  

  • Update of maintenance program (efficiency and robustness improvements) 

  • Ability to install fully from command line 

MedeA 3.9      May 2024 

 

Description of MedeA 3.9 New Features and Enhancements  

 

1. Builders and Editors: 

 

  • Enhancements in exporting SVG files 

  • OpenBabel update 

  • Amorphous Materials Builder: 

    • Improved handling of removed components  

    • New compress layer functionality for quick and robust use, interactively and in a flowchart, for building layers at the desired density  

  • Updates to trajectories handling 

  • Extended Stack Layers builder to allow for stacking triclinic cells 

  • Ability to create repeat units from SMILES 

  • Enhancements for mass criterion when creating Subsets  

  • Microstructure builder: 

    • Weighted seed & growth to create grains of different volume distributions 

    • Option to create columnar slab geometries and rotations around z-axis only 

    • Flowchart stage for builder to be used in a flowchart 

2. Engines: 

 

  • VASP: 

    • Update to the latest release VASP 6.4.3 with many enhancements and bug fixes 

    • New OpenACC-based GPU version which now supports all features of the CPU version 

    • Added support for new VASP 64 potentials. Users can choose their own default and switch easily between 54 and 64 potentials 

    • Added support for the revPBE density functional from the user interface 

    • Added support for further Van der Waals density functionals from the user interface: vdW-DF-cx, rVV10, r2SCAN+rVV10, PBE+rVV10L 

    • Added support for further meta-GGA functionals from the user interface: SCAN-L, rSCAN-L, r2SCAN-L, v1-sregTM, v2-sregTM, v3-sregTM, v2-sregTM-L, OFR2, local MBJLDA 

    • Added support for further hybrid functionals from the user interface: HSE03, HSEsol, RSHXLDA, RSHXPBE, SCAN0 

    • Added support for the van der Waals corrections Many-body dispersion energy /FI and DFT-ulg from the user interface 

    • Davidson optimization algorithm (non-blocked) available for all simulations 

    • CSVR thermostat for canonical (nVT) ensemble 

    • Enhancements for MLFF Molecular Dynamics simulations and trajectory handling 

    • Substantial speed-up of post-processing of Molecular Dynamics runs 

    • NMR Calculation enhancements: vGv approximation for evaluating the magnetic susceptibility 

 

  • LAMMPS: 

    • Enhancements in NPT, Minimize and Compress Layer stages to allow for the use of variables  

 

  • GIBBS: 

    • Several enhancements for GIBBS trajectories and structure list 

    • visualization 

    • Enhancements for Sorption stage  

 

3. Forcefields: 

  • MLPs: 

    • Added ZBL parameters to SNAP MLPs  

  • MLPG: 

    • New MLP type supported: ACE (New) 

    • Fitting Data manager enhancements 

    • Enhancements to forces' charts 

    • Ability to use variables for hyperparameters 

  • VOTCA (New): New module for coarse-grained forcefield creation from atomistic simulation input (Iterative Boltzmann Inversion and Force Matching methods)  

  • PCFF+: 

    • New atom types and parameters for alkyl borates 

    • Refinement for quaternary carbon c0 nonbond parameters 

    • New atom type for alumina and updated for surface atoms 

    • Addition of bond term and bond increment for alpha carbon in carbonates 

    • Enhancements for oxalatoborate anions and new atom types  

  • ReaxFF

    • Added CHONS ReaxFF parameter set (Mattsson et al.) 

  • New torsion terms for use with UFF in LAMMPS 

 

4. Property modules: 

  • UNCLE: 

    • Improvements to message handling, initial and final structure reporting, and checks for the number of requested structures 

    • Enhancements for Optimization stage 

  • P3C: 

    • Enhancements for computation of X3 and X10 descriptors, and perception of ortho/meta geometries  

  • Phonon: 

    • Enhancements for computations using NNP (MLP) forcefields 

  • MD Phonon: 

    • Added Etot_QC, sum of MD total energy and the quantum correction of the vibrational energy 

    • Added Atotal, the total vibrational Helmholtz free energy, which is calculated with Etot_QC - Svib T  

    • Enhanced support of Job restart functionality   

  • Polymer Expert: 

    • Enhanced handling of messages and warnings issued 

  • Deposition: 

    • Enhancement for use of variables to define regions   

 

6. JobServer/TaskServer: 

  • Extended Job submission dialog to include summary regarding the JobServer chosen, the input structure and the active forcefield 

  • Extended Job submission dialog to include Queuing System options 

  • Extended TaskServer for GPU device selection  

  • Enhanced database performance  

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)

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

MedeA 3.0    31 October 2019

 

MedeA 3.0 features: 
 

  • A complete user interface (UI) refresh with updated icons, improved user experience with responsive dialogs, and enhanced operating system compliance on both Windows and Linux improving usability and enabling users to conduct cutting edge research with maximal efficiency,

  • Builder capability extensions - facilitating the creation of complex crystalline and amorphous systems, 

  • A new module (Molecular Descriptors) - providing easy access to numerous topological and geometrical descriptors, in High-Throughput mode,

  • Updates to the MedeA Forcefield library with new forcefield types and parameter sets and extensions broadening coverage and improving simulation accuracy, 

  • Use of reactive forcefields to simulate deposition and etching processes, 

  • Calculation and Analysis extensions for Optical Spectra - providing the ability to predict colors of metals 

 

Description of MedeA 3.0 new features and enhancements

 

General

  • New GUI theme, identical on Linux and Windows

  • Enhanced high resolution and multi-screen support

  • Full compatibility with previous MedeA releases

  • Extensive and intensive documentation upgrades and updates

  • Visualization: new options for lighting

 

Builders and Editors

 

  • MedeA's Molecular and Crystal Builders: 

    • Fragments attachment (e.g. for passivation of a surface)

  • MedeA Amorphous Materials Builder: 

    • Coarse-grained systems support (use mass from forcefield file)

    • Updated orientation biasing for oriented film construction

    • Provision of both saved specific and immediate build options

 

Engines

 

  • MedeA VASP

    • Updated work function results handling in Flowcharts

    • Enhanced support for optical spectra and color prediction

    • Drude conductivity for optical properties of metals 

    • Automatic use of suitably fine energy grids for optical spectra calculations

  • MedeA LAMMPS

    • Improvements for switching between 3D and 2D periodicity

    • Default variables in all LAMMPS stages

    • Added support on NVIDIA GPUs

  • MedeA GIBBS

    • Complete final system update via .sci file

  • MedeA MOPAC 

    • Custom stage for fully customized MOPAC simulations

    • Extra Input enabled for all MOPAC flowchart stages

 

Property Modules

 

  • MedeA Electronics 

    • Access to the energy increment for numerical integration from the GUI of MedeA Electronics to fine-tune transport properties

    • Automated positioning of the Fermi level into the center of the gap for the derivation of transport properties

    • Additional transport functions: electronic fitness functions, inverse transport effective masses

  • MedeA QT

    • Complete handling of datasets with non-existing descriptors

    • Updated multi-row selection and editing capabilities

  • MedeA Deposition

    • Ability to use reactive forcefields to simulate deposition and etching processes

  • MedeA ForceField Optimizer (FFO)

    • Added support for ReaxFF potential

    • Improvements for Tersoff potential optimization

 

High-throughput

 

  • MedeA HT-Descriptors (New) 

    • HT-Descriptors for molecular species can now be easily calculated for the members of a structure list and used in creating QSPR/QSAR correlations, using MedeA QT.  

 

Forcefields

 

  • pcff+ : Forcefield extensions for: 

    • Al2O3 

    • alkyl-arsines 

    • Carboxylic esters 

    • cloro/fluoro hydrocarbons (HCFCs)

    • graphene oxide 

    • silica-siloxane interfacial regions

  • TraPPE-UA+: Forcefield extensions for: 

    • cyclic hydrocarbons 

    • alkyl-arsines

  • MedeA COMB3 & MedeA ReaxFF: addition of descriptions and parameters 

 

Analysis Tools

 

  • MedeA's Optical Spectra 

    • Automatic differentiation between optical properties of metals and semiconductors/insulators, as identified by VASP post-processing

    • Automatically retain the Drude conductivity from VASP post-processing

    • Automatically add Drude term for metallic systems, making use of the default Drude conductivity as calculated by VASP

    • Added transmission coefficient as a function of wave length and slab thickness

    • Attenuation and absorption coefficient

    • Enable customization of energy/wavelengths units

    • Visual color prediction upon reflection and transmission, for direction dependent optically anisotropic materials

    • CIE 1931 and 1964 color spaces upon reflection and transmission (direction dependent in case of optical anisotropy)

 

MedeA's JobServer & TaskServer

 

  • Enhanced MedeA JobServer performance (asynchronous, non blocking mode) 

  • Extensions for HTTPS support 

MedeA 2.22.6    5 December 2018

    1. LAMMPS deposition module

MedeA 2.22.5    12 November 2018

    1. MedeA-QT available for Windows and Linux

    2. MedeA-Phonon:

        - Thermodynamic functions available as variables from the Phonon stage

    3. MedeA-MT:

        - Thermal expansion: Grueneisen parameter calculated from elastic moduli according to Sanditov et al.

        - Option to control large files

        4. Various fixes and enhancements

MedeA 2.22.4    11 May 2018​

    1. Permit installation into directory containing spaces in path

MedeA 2.22.3    19 Apr 2018

        1. Gibbs:

        - extension of sorption stages to use "active system" for the solid

        - addition of final structure files (sci) for all GIBBS stages (including predefined subsets)

        2. JobServer:

        - increase robustness during start

    3. TaskServer:

        - added/extended options on how to control computing resources

            - catch and edge case when terminating task

        5. Electronic Transport:

        - proper scaling for Seebeck tensor

MedeA 2.22.2  30 Mar 2018

        1. MOPAC:

                - improvements on handling of the number of processors 

        2. LAMMPS:

                - addition of fix for image flags (cell offsets)

                - QEq options for COMB3, ReaXFF and EAM/Coul

        3. GIBBS:

                - fix for atomtypes ending with an apostrophe

                - sorbent set from active system

                - additional printable variables for sorption stages

        4. VASP:

                - enable additional input files or replacements for standard input files

                - post-processing enhancements

        5. Thermoset Builder:

                - additional printable variables

                - support of spaces in crosslink subset names

        6. Forcefields:

                - added hybrid ReaxFF/ZBL forcefield type

        7. TaskServer:

                - several improvements in the handling of tasks

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