MedeA’s Builders

The MedeA Environment includes a rich set of builders for many types of systems and applications. Use MedeA’s Builders for constructing atomic-scale models of hard, soft or fluid materials. Work with crystalline or amorphous materials, bulk or surface systems, defect structures, molecules, nanostructures and adsorbates. Complementing MedeA’s standard building capabilities are several specialized modules for building complex and hybrid materials such as amorphous materials, cross-linked polymers or composite structures. In addition, MedeA offers tools to construct heterogeneous interfaces, grain boundaries, and for docking molecules in microporous structures.

MedeA’s Standard Builders

MedeA’s Specialty Builders

MedeA’s Standard Builders

MedeA’s Crystal Builder Part of the standard MedeA Environment

Use MedeA’s Crystal Builder to edit and modify periodic structures retrieved from MedeA’s experimental structure databases. While this is the most convenient way of constructing a periodic structure in MedeA, you can also build crystalline systems from scratch by selecting the desired space group and adding elements at Wyckhoff positions. You may set or change cell parameters, replace or move atoms, set magnetic moments and masses, and freeze selected atomic degrees of freedom. Let MedeA determine a given system’s symmetry, while you choose an appropriate representation, i.e. P1, primitive cell, or highest available symmetry.

MedeA’s Crystal Builder features include:

• Display and edit crystal structures from MedeA’s InfomaticA
• Find symmetry and add atoms at Wyckhoff positions
• Edit cell dimensions and angles
• Edit elements, move atoms and freeze atomic degrees of freedom
• Assign masses and magnetic moments

MedeA’s Molecular Builder Part of the standard MedeA Environment

MedeA Molecular Builder lets you import and edit molecular systems, or build them stepwise using MedeA’s molecular fragment library. Simply paste SMILES code from external sources into the builder, and clean up the resulting molecular systems by running minimizations or short molecular dynamics interactively. Create periodic systems from molecules, or split periodic structures into molecular components. Use building blocks from MedeA’s fragment library to construct complex systems, define polymer backbones and store your own structures for later reference.

MedeA’s Molecular Builder features include:

• SMILES input
• Convenient Insertion mode: Load cursor with atom or molecular fragment, click to add freely or dock to active bonds
• Internal coordinates representation and modification (see datasheet for more details)

MedeA’s Conformer Search Part of the standard MedeA Environment

Search for lowest lying conformers of any type of organic molecular input structure. Display selected systems or create a structure list from all results or selected subsets.

MedeA’s Conformer Search features include:

• SMILES input
• Several search algorithms
• Genetic algorithms and UFF94 forcefield
• Weighted search
• Systematic search

MedeA’s Supercell Builder Part of the standard MedeA Environment

Use MedeA’s Supercell Builder to quickly generate larger cells, multiples of the chemical unit cell in selected directions. Build elongated cells by defining a range parameter or transform unit-cell coordinate axes to create a custom coordinate base.

MedeA’s Supercell Builder features include:

• Simple: Define multiples in each lattice direction
• Automatic: Provide a range parameter for all or selected directions
• Custom: Use a transformation matrix to define a new lattice

MedeA’s Special Quasirandom Structures (SQS) Part of the standard MedeA Environment

Use MedeA’s Special Quasi Random Structures (SQSs) as a simple means to model alloys. With a rather small number of atoms, SQSs mimic the physically most relevant radial correlation functions of a perfectly random structure. Simply select ‘SQS’ from the builder menu and edit starting lattice parameters.

MedeA’s SQS Builder features include:

• Binary: fcc, bcc, hcp
• Ternary: fcc, bcc, B2
• Pseudo-ternary: Zincblende-64 structures

MedeA’s Polymer Builder Part of the standard MedeA Environment

MedeA’s Polymer Builder creates models of isolated polymer chains, providing a foundation for building more complex models. Examples include bulk polymers, blends, solutions, or multiphase systems incorporating one or more interfacial regions.

MedeA’s Polymer Builder features include:

• Extensive Polymer repeat unit library
• Customized repeat units from monomers
• Handles tacticity, repeat unit orientation
• Builds alternating, random and block copolymers
• (see datasheet for more details)

MedeA’s Nanobuilder Part of the standard MedeA Environment

With MedeA’s Nanobuilder, you can construct nano-sized structures of various shapes. With just a few mouse clicks, build spheres, cylinders, tubes, wraps or wires by simply selecting from a handful of input parameters such as element type, chirality, orientation, packing and degree of nesting!

MedeA’s Nanobuilder features include:

• Interactive GUI-based Builder
• Intuitive design criteria guiding construction
• Many shapes and geometries supported
• Full integration with other MedeA builders and modules

MedeA’s Surface Builder Part of the standard MedeA Environment

MedeA’s Surface Builder provides an intuitive way for constructing surface models by cleaving a bulk system. Start with a periodic chemical unit cell loaded from InfomaticA. Select cleavage direction, layer thickness and vacuum thickness. MedeA displays the corresponding surface slab model. If desired, use upper and lower cleavage planes to control surface termination, find new symmetry and apply to create your final surface slab model. Use cell transformation and supercell builder to increase surface plane area, e.g. for construction of adsorbate-adsorbent models.

MedeA’s Surface Builder features include:

• Choose Miller indices, material thickness and vacuum layer thickness
• Preview and edit surface slab model
• Control surface termination and modify vacuum layer thickness

MedeA’s Stack Layer Builder Part of the standard MedeA Environment

MedeA’s Stack Layer Builder is designed for preparation of interface systems comprising two or more layers of materials. You may combine individual layers of amorphous and crystalline nature, solids, liquids, partially ordered liquid crystal systems and vacuum regions. The builder can process organic, inorganic or metallic systems.

MedeA’s Stack Layer Builder features include:

• Works with MedeA subsets to allow analysis of specific atoms in layer
• Adjust layers relative to each other
• Control individual layer thickness upon final assembly
• Quick creation of bilayers by in-plane reflection

MedeA’s Substitutional Builder Part of the standard MedeA Environment

MedeA’s Substitutional Search Builder let’s you explore symmetry and structure of systems with substitutional defects. For any type of input systems MedeA lists symmetrically different structures as you replace 1, 2, or more element types. Sort the resulting list by relative weight, symmetry, number of atoms per cell or nearest neighbor distance.

MedeA’s Substitutional Search Builder features include:

• Systematic symmetry analysis of substitutional defect/vacancy structures
• Ranking by structural parameters such as e.g. nearest defect distances
• Produces defect structures ready for DFT total energy calculations

MedeA’s Random Substitutions Part of the standard MedeA Environment

MedeA’s Random Substitutions provides an intuitive way for creating defect or vacancy structures when one or larger numbers of elements need to be replaced. Define a set of rules to perform substitutions repeatedly, create multiple configurations and save results to structure lists for subsequent processing.

MedeA’s Random Substitutions features include:

• Define attributes for atoms to substitute: by name, subset, element type, etc.
• Choose % or define number of substitutions to be performed
• Create multiple configurations and save to structure lists

MedeA’s Specialty Builders

MedeA Amorphous Materials Builder

The MedeA Amorphous Materials Builder lets you efficiently create condensed phase models based on system chemical composition and target density. It eliminates the need for lengthy mixing and amorphization simulations through realistic sampling of the translational, rotational, and conformational degrees of freedom of component species.

The MedeA Amorphous Materials Builder key benefits and features include:

• Creates realistic configurations of a broad range of materials including
• Polymers and polymer blends
• Small molecule fluids
• Liquid mixtures and electrolytes
• Mixed oxide glass melts (see datasheet for full list)
• Integration with other modules using MedeA’s Flowcharts

Datasheet View Download

MedeA’s Thermoset Builder

MedeA’s Thermoset Builder applies state-of-the-art methods for creating complex topologies of polymer networks in order to create strain-free molecular models with experimentally observed crosslink densities.

MedeA’s Thermoset Builder key features include:

• Full integration into MedeA’s Flowcharts, for batch processing and property averaging
• Rigorous monitoring of material characteristics during crosslinking
• Lets you combine resins, curing agents and solvents
• Creates realistic models for a wide range of thermosets including:
• Epoxies
• Polyesters (alkyds)
• Cyanate esters
• Epoxy-Phenol-Novolac molding compounds
• (see datasheet for full list)

MedeA’s Thermoset Builder is part of the MedeA Amorphous Materials Builder

Datasheet View Download

MedeA Interface Builder

The MedeA Interface Builder lets you create an explicit, atomic-scale interface from two surfaces, allowing for a predefined maximum in-plane mismatch between adjoining layers. The MedeA Interface Builder helps to identify and build twist grain boundaries as well as coherent, and/or semi-coherent interfaces. It produces periodic, commensurate cells, which may be used as direct input for MedeA’s compute work flows, engaging VASP, LAMMPS, or any other engine or building stage. Naturally, you can further edit interface structures in MedeA, e.g. by adding impurities, vacancies and interstitial defects as appropriate.

The MedeA Interface Builder key features include:

• Accounts for relative materials stiffness
• Offers solutions for commensurate cells of different size and symmetry
• Allows exploration of lateral offsets (gamma surface)
• Full integration with MedeA’s Compute Engines and other Modules
• (see datasheet for more detail)

Datasheet View Download