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  

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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

​

​

​

​

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​

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 

• A 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 

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