MedeA® Application Notes for Fundamental Research

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
### [Patrick Soukiassian](, [Erich Wimmer](/about/erich-wimmer), Edvige Celasco, Claudia Giallombardo, Simon Bonanni, Luca Vattuone, Letizia Savio, Anontio Tejeda, Mathieu Silly, Marie D’angelo, Fausto Sirotti, Mario Rocca _Nanostructuring a surface is a key and mandatory engineering step toward advances in nanotechnology. A team of french and italian scientists and of a franco-american company has just shown that hydrogen/deuterium (H/D) induces the opening of nanotunnels below the surface of an advanced semiconductor, silicon carbide (SiC). Such a finding is an especially interesting one, particularly in views of the specific properties of SiC. These investigations have been performed using advanced experimental tools such as synchrotron radiation and vibrational spectroscopy techniques, and state-of-the-art theoretical simulations. Depending on the H/D SiC surface exposures, these nanotunnels undergo through a sequence of semiconducting/metallic/semiconducting transitions. Such nanotunnels open very promising prospects toward applications in electronic, chemistry, storage, sensors and biotechnology._
The compressibility, tensile strength, and mechanical resistance to shear of a solid are related to the corresponding moduli (bulk, Young’s, and shear modulus), which are derived from the coefficients of elasticity. First-principles calculations of these fundamental mechanical properties give values of the same quality as experimental data, but at a substantially smaller effort and cost. This is demonstrated here for cubic silicon carbide, β-SiC, corundum, α-Al₂O₃, and a tourmaline with a fairly complex crystal structure. First-principles calculations are a valuable source for these fundamental materials property data.
Elastic coefficients and moduli for cubic silicon carbide (β-SiC), corundum (α-Al₂O₃), and a tourmaline crystal (Schorl)
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 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/m<sup>2<sup>.
Surface Energy of Molybdenum
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
The purpose of this study is the computation of the cleavage energy of a material, i.e. the energy required to split a material into two parts. This could be a bulk material, a grain boundary, or an interface. To this end, one needs to compute the total energy of the bulk solid and the material with a free surface.
Cleavage Energy of TiN