Julian D. Gale

The SIESTA method for ab initio order-N materials simulation

We have developed and implemented a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical linear combination of atomic orbitals basis set, which includes multiple-zeta and polarization orbitals. Exchange and correlation are treated with the local spin density or generalized gradient approximations. The basis functions and the electron density are projected on a real-space grid, in order to calculate the Hartree and exchange-correlation potentials and matrix elements, with a number of operations that scales linearly with the size of the system. We use a modified energy functional, whose minimization produces orthogonal wavefunctions and the same energy and density as the Kohn-Sham energy functional, without the need for an explicit orthogonalization. Additionally, using localized Wannier-like electron wavefunctions allows the computation time and memory required to minimize the energy to also scale linearly with the size of the system. Forces and stresses are also calculated efficiently and accurately, thus allowing structural relaxation and molecular dynamics simulations.An efficient method is described to handle mesh indexes in multidimensional problems like numerical integration of partial differential equations, lattice model simulations, and determination of atomic neighbor lists. By creating an extended mesh, beyond the periodic unit cell, the stride in memory between equivalent pairs of mesh points is independent of their position within the cell. This allows to contract the mesh indexes of all dimensions into a single index, avoiding modulo and other implicit index operations.

GULP: A computer program for the symmetry-adapted simulation of solids

Algorithms for the symmetry-adapted energy minimisation of solids using analytical first and second derivatives have been devised and implemented in a new computer program GULP. These new methods are found to lead to an improvement in computational efficiency of up to an order of magnitude over the standard algorithm, which takes no account of symmetry, the largest improvement being obtained from the use of symmetry in the generation of the hessian. Accelerated convergence techniques for the dispersion energy are found to be beneficial in improving the precision at little extra computational cost, particularly when a one centre decomposition is possible or the Ewald sum weighting towards real-space is increased.

The general utility lattice program (GULP)

The General Utility Lattice Program (GULP) has been extended to include the ability to simulate polymers and surfaces, as well as adding many other new features, and the current status of the program is fully documented. Both the background theory is described, as well as providing a concise review of some of the previous applications in order to demonstrate the range of its use. Examples are presented of work performed using the new compatibilities of the software, including the calculation of Born effective charges, mechanical properties as a function of applied pressure, calculation of frequency-dependent dielectric data, surface reconstructions of calcite and the performance of a linear-scaling algorithm for bond-order potentials.

The SIESTA method; developments and applicability

Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.

Stable prenucleation mineral clusters are liquid-like ionic polymers

Calcium carbonate is an abundant substance that can be created in several mineral forms by the reaction of dissolved carbon dioxide in water with calcium ions. Through biomineralization, organisms can harness and control this process to form various functional materials that can act as anything from shells through to lenses. The early stages of calcium carbonate formation have recently attracted attention as stable prenucleation clusters have been observed, contrary to classical models. Here we show, using computer simulations combined with the analysis of experimental data, that these mineral clusters are made of an ionic polymer, composed of alternating calcium and carbonate ions, with a dynamic topology consisting of chains, branches and rings. The existence of a disordered, flexible and strongly hydrated precursor provides a basis for explaining the formation of other liquid-like amorphous states of calcium carbonate, in addition to the non-classical behaviour during growth of amorphous calcium carbonate.

Water Is the Key to Nonclassical Nucleation of Amorphous Calcium Carbonate

Calcium carbonate is a ubiquitous mineral that represents one of the most significant biominerals, a major contributor to carbon sequestration through geological deposits, and a technological hindrance as a result of scale formation. Amorphous calcium carbonate is intimately involved in the nucleation and growth of this material, yet much remains undiscovered regarding the atomic detail. Through dynamical simulation we demonstrate that nucleation of amorphous calcium carbonate follows a nonclassical pathway. This arises from the addition of ion pairs to clusters exhibiting a consistently exothermic free energy that persists with increasing particle size. Furthermore, the disruption of the surrounding water of solvation by the atomically rough surface reduces the barrier to growth to the order of ambient thermal energy, thereby allowing the amorphous phase to grow faster than crystalline polymorphs. Amorphous calcium carbonate nanoparticles are also found to exploit size-dependent water content to render itself more stable than the favored bulk phase, calcite, below a critical diameter of close to 4 nm.

Empirical potential derivation for ionic materials

Abstract A program has been developed for the derivation of empirical interatomic potentials, with particular regard to ionic materials and the use of shell models, incorporating two new methods of fitting. Concurrent fitting of multiple structures is found to enhance greatly the reliability of the derived potentials and can lead to a physically sensible O-O potential without the use of constraints. Inclusion of gas-phase cluster information appears to be beneficial even within an ionic model. By combining free-energy minimization with empirical fitting based on displacements, rather than gradients, it is now possible to determine interatomic potentials with correct treatment of thermal effects and the zero-point energy.

Microscopic Evidence for Liquid-Liquid Separation in Supersaturated CaCO3 Solutions

Making Crystals The initial transition from a disordered solution to the formation of nuclei that grow into crystals continues to be a puzzle. Recent experiments suggested the formation of stable ordered clusters that appear prior to the formation of the first nuclei. Wallace et al. (p. 885; see the Perspective by Myerson and Trout) used molecular dynamics to look at the potential structure and dynamics of these clusters and lattice gas simulations to explore the population dynamics of the cluster populations prior to nucleation. A liquid-liquid phase separation process was observed whereby one phase becomes more concentrated in ions and becomes the precursor for nuclei to form. The preordering seen during calcium carbonate crystallization may be due to a liquid-liquid separation process. [Also see Perspective by Myerson and Trout] Recent experimental observations of the onset of calcium carbonate (CaCO3) mineralization suggest the emergence of a population of clusters that are stable rather than unstable as predicted by classical nucleation theory. This study uses molecular dynamics simulations to probe the structure, dynamics, and energetics of hydrated CaCO3 clusters and lattice gas simulations to explore the behavior of cluster populations before nucleation. Our results predict formation of a dense liquid phase through liquid-liquid separation within the concentration range in which clusters are observed. Coalescence and solidification of nanoscale droplets results in formation of a solid phase, the structure of which is consistent with amorphous CaCO3. The presence of a liquid-liquid binodal enables a diverse set of experimental observations to be reconciled within the context of established phase-separation mechanisms.

Calcium Carbonate Polyamorphism and Its Role in Biomineralization: How Many Amorphous Calcium Carbonates Are There?

Although the polymorphism of calcium carbonate is well known, and its polymorphs--calcite, aragonite, and vaterite--have been highly studied in the context of biomineralization, polyamorphism is a much more recently discovered phenomenon, and the existence of more than one amorphous phase of calcium carbonate in biominerals has only very recently been understood. Here we summarize what is known about polyamorphism in calcium carbonate as well as what is understood about the role of amorphous calcium carbonate in biominerals. We show that consideration of the amorphous forms of calcium carbonate within the physical notion of polyamorphism leads to new insights when it comes to the mechanisms by which polymorphic structures can evolve in the first place. This not only has implications for our understanding of biomineralization, but also of the means by which crystallization may be controlled in medical, pharmaceutical, and industrial contexts.

The prediction of inorganic crystal structures using a genetic algorithm and energy minimisation

A genetic algorithm has been used to generate plausible crystal structures from the knowledge of only the unit cell dimensions and constituent elements. We successfully generate 38 known binary oxides and various known ternary oxides with the Perovskite, Pyrochlore and Spinel structures, from starting configurations which include no knowledge of the atomic arrangement in the unit cell. The quality of the structures is initially assessed using a cost function which is based on the bond valence model with a number of refinements. The lattice energy, based on the Born model of a solid, is minimised using a local optimiser for the more plausible candidate structures. The method has been implemented within the computational package GULP. An extensive collection of Buckingham potential parameters for use in such simulations on metal oxides is also tabulated.