MedeA® Application Notes for Universities

This application note provides an overview of the forcefield based simulation of crystalline C₆₀ (Buckminsterfullerene) using the LAMMPS molecular dynamics simulation package. The emphasis is on the overall philosophy of LAMMPS calculations in the MedeA® environment.

We demonstrate the capabilities of MedeA with selected examples, focusing on the lattice thermal
conductivity using forcefield methods as implemented in the software environment. The thermal conductivity is of high interest in different fields. In thermoelectrics, materials are sought with a high electrical conductivity combined with a low thermal conductivity as can be found in doped semiconductors with a high density of states near the band edges. In the present paper, we investigate the thermal conductivity of Si-Ge alloys and discuss the influence of defects, and disorder. All the computations are done using MedeA's LAMMPS and Thermal Conductivity modules, with the Reverse Non-Equilibrium Molecular Dynamics (RNEMD) approach.

Lattice thermal conductivity calculations in Si-Ge

The crystal structure of a purely organic, hydrogen-bonded molecular crystal is very well described by density functional theory with a gradient-corrected Perdew-Becke-Ernzerhof potential. The computations were preformed with the VASP program using the projector augmented wave method with a plane wave basis set. The agreement between computed and experimental lattice parameters is better than 2% with a tendency of the calculations to overestimate the bond lengths. The calculations provide equilibrium positions for the hydrogen atoms, which are difficult to place based on x-ray diffraction data.

Crystal Structure of Glucose: Placing Hydrogen Atoms by Computations

The energy of adsorption and dissociation of molecules on surfaces plays a critical role in technological processes such as chemical vapor deposition, catalysis, and corrosion. The present case shows the calculation of the energy of the dissociative chemisorption of a silane molecule on a Si (001) surface.

Energy of Dissociative Chemisorption of SiH₄ on Si (001) Surface

This application shows the interaction of carbon monoxide with rutile.
An answer is given to the question whether CO binds with the carbon or the oxygen molecule to the surface.

CO Adsorption on a TiO₂ Surface

The molecular builder (Molecular Builder) is part of the MEDEA standard suite of building tools. This tutorial provides an overview of the Molecular Builder’s basic functionality.

In this application note, we show how to build the isomers ethyl alcohol and di-ethyl ether and calculate their respective heats of formation.

Heat of Formation of Ethyl Alcohol and Dimethyl Ether

The surface energy of a material is defined as the energy required to create a surface (h k l) from the bulk material. Surface energies are usually given in units of J/m2.

Surface Energy of Molybdenum

The correct lattice parameters of a crystalline structure are of fundamental importance for any reliable computational predictions of materials properties. This case study shows the calculation of the lattice parameters of titanium carbide, TiC.

Structure of bulk Titanium Carbide (TiC)

This application note deals with positioning molecules on surfaces. As an example we will investigate the adsorption of ethyl alcohol (ethanol) on a Cu (111) surface. In doing so we will consider two possible configurations for the adsorbed molecule:
1. adsorbed ethanol
2. dehydrogenated ethanol, i.e. an ethoxygen.
Running structure relaxations using VASP produces a first estimate of the relative stability of these two systems.

Dehydrogenation Energy of Ethyl Alcohol (Ethanol) on a Cu (111) Surface

This case study covers the practical use of MEDEA to calculate thermochemical functions for solids, molecules and atoms. We will use VASP and PHONON for this, but the current document focuses on the thermochemistry and not the details of the calculations.

Practical Thermochemistry: Sodium Metal, Chlorine Gas, and Solid Sodium  Chloride

Despite the enormous progress in experimental surface science, notably with spectroscopic
methods exploiting synchrotron radiation and scanning tunneling microscopy, computations
remain one of the most useful sources for accurate data on surface structures. In fact, quite often
it is the combination of experimental and computed results, which gives the most reliable data of
surface structures. As an example, let us apply MEDEA to the Si(001) surface. This surface is the
typical substrate in the manufacturing of semiconducting devices.

Surface Reconstruction of Si(001)

Ferromagnetism has its quantum mechanic origin in the difference of spin-up and spin-down
electron densities. It is driven by a balance between a gain in exchange energy due to larger spin-
polarization and a loss in Coulomb repulsion and kinetic energy of the electron system.

In Chromium and Chromium alloys antiferromagnetic ordering and spin-density-waves (SDW) states are at the origin of many physical properties like thermal expansion, elastic constants, and electrical resistivity among others.
This document summarizes structural and elastic properties of Chromium, computed from
first principles.

Chromium: Structure and Elastic Properties

The convergence of the total electronic energy as computed with VASP is determined by two key
computational parameters, namely the number of basis functions (plane wave cutoff) and the
number of k-points (k-spacing). In addition the integration of the states near the Fermi level is
influenced by a smearing parameter.

Convergence of Total Energy with Plane Wave Cutoff and k-Mesh:  Mo, Al, and LiF

The cohesive energy of a solid is defined as the energy required for separating the condensed material into isolated free atoms. Cohesive energies range from about 0.1 eV or 10 kJ/mol for inert gases up to about 8 eV or 800 kJ/mol per atom for strongly bound materials such as diamond or tungsten.

Cohesive Energy of Diamond