A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids under external stress and at finite temperature. As an example of the use of this technique we show how a single crystal of Ni behaves under uniform uniaxial compressive and tensile loads. This work confirms some of the results of static (i.e., zero temperature) calculations reported in the literature. We also show that some results regarding the stress‐strain relation obtained by static calculations are invalid at finite temperature. We find that, under compressive loading, our model of Ni shows a bifurcation in its stress‐strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal close packing. It is suggested that such a transformation could perhaps be observed experimentally under extreme conditions of shock.

Polymorphic transitions in single crystals: A new molecular dynamics method

A model potential-energy function comprising both two- and three-atom contributions is proposed to describe interactions in solid and liquid forms of Si. Implications of this potential are then explored by molecular-dynamics computer simulation, using 216 atoms with periodic boundary conditions. Starting with the diamond-structure crystal at low temperature, heating causes spontaneous nucleation and melting. The resulting liquid structurally resembles the real Si melt. By carrying out steepest-descent mappings of system configurations onto potential-energy minima, two main conclusions emerge: (1) a temperature-independent inherent structure underlies the liquid phase, just as for ``simple'' liquids with only pair interactions; (2) the Lindemann melting criterion for the crystal apparently can be supplemented by a freezing criterion for the liquid, where both involve critical values of appropriately defined mean displacements from potential minima.

Computer simulation of local order in condensed phases of silicon

Self-Assembly of Discrete Cyclic Nanostructures Mediated by Transition Metals

MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson–Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, rele...

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.

Recent theoretical work on the microscopic structure and surface tension of the liquid-vapour interface of simple (argon-like) fluids is critically reviewed. In particular, the form of pairwise intermolecular correlations in the liquid surface and the capillary wave treatment of the interface are examined in some detail. It is argued that conventional capillary wave theory, which leads to divergences in the width of the density profile, is unsatisfactory for describing all the equilibrium aspects of the interface. The density functional formalism which has been developed to study the liquid-vapour interface can also be profitably applied to other problems in the statistical mechanics of non-uniform fluids; here a new generalization of the ‘linear’ theory of spinodal decomposition is formulated and by considering a ‘nearly uniform’ fluid, some useful results for the long-wavelength behaviour of the liquid structure factor of various monatomic liquids are obtained. Some other topics of current inte...

The nature of the liquid-vapour interface and other topics in the statistical mechanics of non-uniform, classical fluids

Introduction. Statistical Mechanics and Molecular Distribution Functions. Computer "Experiments" on Liquids. Diagrammatic Expansions. Distribution Function Theories. Perturbation Theories. Time-dependent Correlation Functions and Response Functions. Hydrodynamics And Transport Coefficients. Microscopic Theories of Time-Correlation Functions. Ionic Liquids. Simple Liquid Metals. Molecular Liquids. Appendices. References. Index.

J.‐P. Hansen

Papers

Theory of simple liquids