arXiv subjects

M. J. Gillan

Publications and source records attributed to M. J. Gillan.

At least 19 recordsLinked to original sources

arXiv2016

Perspective: How good is DFT for water?

Kohn-Sham density functional theory (DFT) has become established as an indispensable tool for investigating aqueous systems of all kinds, including those important in chemistry, surface science, biology and the earth sciences. Nevertheless, many widely used approximations for the exchange-correlation (XC) functional describe the properties of pure water systems with an accuracy that is not fully satisfactory. The explicit inclusion of dispersion interactions generally improves the description, but there remain large disagreements between the predictions of different dispersion-inclusive methods. We present here a review of DFT work on water clusters, ice structures and liquid water, with the aim of elucidating how the strengths and weaknesses of different XC approximations manifest themselves across this variety of water systems. Our review highlights the crucial role of dispersion in describing the delicate balance between compact and extended structures of many different water systems, including the liquid. By referring to a wide range of published work, we argue that the correct description of exchange-overlap interactions is also extremely important, so that the choice of semi-local or hybrid functional employed in dispersion-inclusive methods is crucial. The origins and consequences of beyond-2-body errors of approximate XC functionals are noted, and we also discuss the substantial differences between different representations of dispersion. We propose a simple numerical scoring system that rates the performance of different XC functionals in describing water systems, and we suggest possible future developments.

cond-mat.mtrl-sci↗

arXiv2013

Density-functional theory study of gramicidin A ion channel geometry and electronic properties

Understanding the mechanisms underlying ion channel function from the atomic-scale requires accurate ab initio modelling as well as careful experiments. Here, we present a density functional theory (DFT) study of the ion channel gramicidin A, whose inner pore conducts only monovalent cations and whose conductance has been shown to depend on the side chains of the amino acids in the channel. We investigate the ground-state geometry and electronic properties of the channel in vacuum, focusing on their dependence on the side chains of the amino acids. We find that the side chains affect the ground state geometry, while the electrostatic potential of the pore is independent of the side chains. This study is also in preparation for a full, linear scaling DFT study of gramicidin A in a lipid bilayer with surrounding water. We demonstrate that linear scaling DFT methods can accurately model the system with reasonable computational cost. Linear scaling DFT allows ab initio calculations with 10,000 to 100,000 atoms and beyond, and will be an important new tool for biomolecular simulations.

q-bio.BM↗

arXiv2013

Energy benchmarks for water clusters and ice structures from an embedded many-body expansion

We show how an embedded many-body expansion (EMBE) can be used to calculate accurate \emph{ab initio} energies of water clusters and ice structures using wavefunction-based methods. We use the EMBE described recently by Bygrave \emph{et al.} (J. Chem. Phys. \textbf{137}, 164102 (2012)), in which the terms in the expansion are obtained from calculations on monomers, dimers, etc. acted on by an approximate representation of the embedding field due to all other molecules in the system, this field being a sum of Coulomb and exchange-repulsion fields. Our strategy is to separate the total energy of the system into Hartree-Fock and correlation parts, using the EMBE only for the correlation energy, with the Hartree-Fock energy calculated using standard molecular quantum chemistry for clusters and plane-wave methods for crystals. Our tests on a range of different water clusters up to the 16-mer show that for the second-order Møller-Plesset (MP2) method the EMBE truncated at 2-body level reproduces to better than 0.1 m$E_{\rm h}$/monomer the correlation energy from standard methods. The use of EMBE for computing coupled-cluster energies of clusters is also discussed. For the ice structures Ih, II and VIII, we find that MP2 energies near the complete basis-set limit reproduce very well the experimental values of the absolute and relative binding energies, but that the use of coupled-cluster methods for many-body correlation (non-additive dispersion) is essential for a full description. Possible future applications of the EMBE approach are suggested.

cond-mat.mtrl-sci↗

arXiv2013

First-principles energetics of water: a many-body analysis

Standard forms of density-functional theory (DFT) have good predictive power for many materials, but are not yet fully satisfactory for solid, liquid and cluster forms of water. We use a many-body separation of the total energy into its 1-body, 2-body (2B) and beyond-2-body (B2B) components to analyze the deficiencies of two popular DFT approximations. We show how machine-learning methods make this analysis possible for ice structures as well as for water clusters. We find that the crucial energy balance between compact and extended geometries can be distorted by 2B and B2B errors, and that both types of first-principles error are important.

cond-mat.mtrl-sci↗

arXiv2012

Assessing the accuracy of quantum Monte Carlo and density functional theory for energetics of small water clusters

We present a detailed study of the energetics of water clusters (H$_2$O)$_n$ with $n \le 6$, comparing diffusion Monte Carlo (DMC) and approximate density functional theory (DFT) with well converged coupled-cluster benchmarks. We use the many-body decomposition of the total energy to classify the errors of DMC and DFT into 1-body, 2-body and beyond-2-body components. Using both equilibrium cluster configurations and thermal ensembles of configurations, we find DMC to be uniformly much more accurate than DFT, partly because some of the approximate functionals give poor 1-body distortion energies. Even when these are corrected, DFT remains considerably less accurate than DMC. When both 1- and 2-body errors of DFT are corrected, some functionals compete in accuracy with DMC; however, other functionals remain worse, showing that they suffer from significant beyond-2-body errors. Combining the evidence presented here with the recently demonstrated high accuracy of DMC for ice structures, we suggest how DMC can now be used to provide benchmarks for larger clusters and for bulk liquid water.

cond-mat.mtrl-sci↗

arXiv2011

The kinetics of homogeneous melting beyond the limit of superheating

Molecular dynamics simulation is used to study the time-scales involved in the homogeneous melting of a superheated crystal. The interaction model used is an embedded-atom model for Fe developed in previous work, and the melting process is simulated in the microcanonical $(N, V, E)$ ensemble. We study periodically repeated systems containing from 96 to 7776 atoms, and the initial system is always the perfect crystal without free surfaces or other defects. For each chosen total energy $E$ and number of atoms $N$, we perform several hundred statistically independent simulations, with each simulation lasting for between 500 ps and 10 ns, in order to gather statistics for the waiting time $τ_{\rm w}$ before melting occurs. We find that the probability distribution of $τ_{\rm w}$ is roughly exponential, and that the mean value $<τ_{\rm w} >$ depends strongly on the excess of the initial steady temperature of the crystal above the superheating limit identified by other researchers. The mean $<τ_{\rm w}>$ also depends strongly on system size in a way that we have quantified. For very small systems of $\sim 100$ atoms, we observe a persistent alternation between the solid and liquid states, and we explain why this happens. Our results allow us to draw conclusions about the reliability of the recently proposed Z method for determining the melting properties of simulated materials, and to suggest ways of correcting for the errors of the method.

cond-mat.stat-mech↗

arXiv2010

Bulk and surface energetics of lithium hydride crystal: benchmarks from quantum Monte Carlo and quantum chemistry

We show how accurate benchmark values of the surface formation energy of crystalline lithium hydride can be computed by the complementary techniques of quantum Monte Carlo (QMC) and wavefunction-based molecular quantum chemistry. To demonstrate the high accuracy of the QMC techniques, we present a detailed study of the energetics of the bulk LiH crystal, using both pseudopotential and all-electron approaches. We show that the equilibrium lattice parameter agrees with experiment to within 0.03 %, which is around the experimental uncertainty, and the cohesive energy agrees to within around 10 meV per formula unit. QMC in periodic slab geometry is used to compute the formation energy of the LiH (001) surface, and we show that the value can be accurately converged with respect to slab thickness and other technical parameters. The quantum chemistry calculations build on the recently developed hierarchical scheme for computing the correlation energy of a crystal to high precision. We show that the hierarchical scheme allows the accurate calculation of the surface formation energy, and we present results that are well converged with respect to basis set and with respect to the level of correlation treatment. The QMC and hierarchical results for the surface formation energy agree to within about 1 %.

cond-mat.mtrl-sci↗

arXiv2010

Ab initio statistical mechanics of surface adsorption and desorption: II. Nuclear quantum effects

We show how the path-integral formulation of quantum statistical mechanics can be used to construct practical {\em ab initio} techniques for computing the chemical potential of molecules adsorbed on surfaces, with full inclusion of quantum nuclear effects. The techniques we describe are based on the computation of the potential of mean force on a chosen molecule, and generalise the techniques developed recently for classical nuclei. We present practical calculations based on density functional theory with a generalised-gradient exchange-correlation functional for the case of H$_2$O on the MgO~(001) surface at low coverage. We note that the very high vibrational frequencies of the H$_2$O molecule would normally require very large numbers of time slices (beads) in path-integral calculations, but we show that this requirement can be dramatically reduced by employing the idea of thermodynamic integration with respect to the number of beads. The validity and correctness of our path-integral calculations on the H$_2$O/MgO~(001) system are demonstrated by supporting calculations on a set of simple model systems for which quantum contributions to the free energy are known exactly from analytic arguments.

cond-mat.mtrl-sci↗

arXiv2009

Melting properties of a simple tight-binding model of transition metals: I.The region of half-filled d-band

We present calculations of the free energy, and hence the melting properties, of a simple tight-binding model for transition metals in the region of d-band filling near the middle of a d-series, the parameters of the model being designed to mimic molybdenum. The melting properties are calculated for pressures ranging from ambient to several Mbar. The model is intended to be the simplest possible tight-binding representation of the two basic parts of the energy: first, the pairwise repulsion due to Fermi exclusion; and second, the d-band bonding energy described in terms of an electronic density of states that depends on structure. In addition to the number of d-electrons, the model contains four parameters, which are adjusted to fit the pressure dependent d-band width and the zero-temperature pressure-volume relation of Mo. We show that the resulting model reproduces well the phonon dispersion relations of Mo in the body-centred-cubic structure, as well as the radial distribution function of the high-temperature solid and liquid given by earlier first-principles simulations. Our free-energy calculations start from the free energy of the liquid and solid phases of the purely repulsive pair-potential model, without d-band bonding. The free energy of the full tight-binding model is obtained from this by thermodynamic integration. The resulting melting properties of the model are quite close to those given by earlier first-principles work on Mo. An interpretation of these melting properties is provided by showing how they are related to those of the purely repulsive model.

cond-mat.mtrl-sci↗

arXiv2008

Comment on 'Molybdenum at High Pressure and Temperature: Melting from Another Solid Phase'

There has been a major controversy over the past seven years about the high-pressure melting curves of transition metals. Static compression (diamond-anvil cell: DAC) experiments up to the Mbar region give very low melting slopes dT_m/dP, but shock-wave (SW) data reveal transitions indicating much larger dT_m/dP values. Ab initio calculations support the correctness of the shock data. In a very recent letter, Belonoshko et al. propose a simple and elegant resolution of this conflict for molybdenum. Using ab initio calculations based on density functional theory (DFT), they show that the high-P/high-T phase diagram of Mo must be more complex than was hitherto thought. Their calculations give convincing evidence that there is a transition boundary between the normal bcc structure of Mo and a high-T phase, which they suggest could be fcc. They propose that this transition was misinterpreted as melting in DAC experiments. In confirmation, they note that their boundary also explains a transition seen in the SW data. We regard Belonoshko et al.'s Letter as extremely important, but we note that it raises some puzzling questions, and we believe that their proposed phase diagram cannot be completely correct. We have calculated the Helmholtz and Gibbs free energies of the bcc, fcc and hcp phases of Mo, using essentially the same quasiharmonic methods as used by Belonoshko et al.; we find that at high-P and T Mo in the hcp structure is more stable than in bcc or fcc.

cond-mat.mtrl-sci↗

arXiv2008

Zero-temperature generalized phase diagram of the 4d transition metals under pressure

We use an accurate implementation of density functional theory (DFT) to calculate the zero-temperature generalized phase diagram of the 4$d$ series of transition metals from Y to Pd as a function of pressure $P$ and atomic number $Z$. The implementation used is full-potential linearized augmented plane waves (FP-LAPW), and we employ the exchange-correlation functional recently developed by Wu and Cohen. For each element, we obtain the ground-state energy for several crystal structures over a range of volumes, the energy being converged with respect to all technical parameters to within $\sim 1$ meV/atom. The calculated transition pressures for all the elements and all transitions we have found are compared with experiment wherever possible, and we discuss the origin of the significant discrepancies. Agreement with experiment for the zero-temperature equation of state is generally excellent. The generalized phase diagram of the 4$d$ series shows that the major boundaries slope towards lower $Z$ with increasing $P$ for the early elements, as expected from the pressure induced transfer of electrons from $sp$ states to $d$ states, but are almost independent of $P$ for the later elements. Our results for Mo indicate a transition from bcc to fcc, rather than the bcc-hcp transition expected from $sp$-$d$ transfer.

cond-mat.mtrl-sci↗

arXiv2007

Ab initio melting curve of molybdenum by the phase coexistence method

We report ab initio calculations of the melting curve of molybdenum for the pressure range 0-400 GPa. The calculations employ density functional theory (DFT) with the Perdew-Burke-Ernzerhof exchange-correlation functional in the projector augmented wave (PAW) implementation. We present tests showing that these techniques accurately reproduce experimental data on low-temperature b.c.c. Mo, and that PAW agrees closely with results from the full-potential linearized augmented plane-wave implementation. The work attempts to overcome the uncertainties inherent in earlier DFT calculations of the melting curve of Mo, by using the ``reference coexistence'' technique to determine the melting curve. In this technique, an empirical reference model (here, the embedded-atom model) is accurately fitted to DFT molecular dynamics data on the liquid and the high-temperature solid, the melting curve of the reference model is determined by simulations of coexisting solid and liquid, and the ab initio melting curve is obtained by applying free-energy corrections. Our calculated melting curve agrees well with experiment at ambient pressure and is consistent with shock data at high pressure, but does not agree with the high pressure melting curve deduced from static compression experiments. Calculated results for the radial distribution function show that the short-range atomic order of the liquid is very similar to that of the high-T solid, with a slight decrease of coordination number on passing from solid to liquid. The electronic densities of states in the two phases show only small differences. The results do not support a recent theory according to which very low dTm/dP values are expected for b.c.c. transition metals because of electron redistribution between s-p and d states.

cond-mat.mtrl-sci↗

arXiv2007

Ab initio statistical mechanics of surface adsorption and desorption: I. H$_2$O on MgO (001) at low coverage

We present a general computational scheme based on molecular dynamics (m.d.) simulation for calculating the chemical potential of adsorbed molecules in thermal equilibrium on the surface of a material. The scheme is based on the calculation of the mean force in m.d. simulations in which the height of a chosen molecule above the surface is constrained, and subsequent integration of the mean force to obtain the potential of mean force and hence the chemical potential. The scheme is valid at any coverage and temperature, so that in principle it allows the calculation of the chemical potential as a function of coverage and temperature. It avoids all statistical mechanical approximations, except for the use of classical statistical mechanics for the nuclei, and assumes nothing in advance about the adsorption sites. From the chemical potential, the absolute desorption rate of the molecules can be computed, provided the equilibration rate on the surface is faster than the desorption rate. We apply the theory by {\em ab initio} m.d. simulation to the case of H$_2$O on MgO (001) in the low-coverage limit, using the Perdew-Burke-Ernzerhof (PBE) form of exchange-correlation. The calculations yield an {\em ab initio} value of the Polanyi-Wigner frequency prefactor, which is more than two orders of magnitude greater than the value of $10^{13}$ s$^{-1}$ often assumed in the past. Provisional comparison with experiment suggests that the PBE adsorption energy may be too low, but the extension of the calculations to higher coverages is needed before firm conclusions can be drawn. The possibility of including quantum nuclear effects by using path-integral simulations is noted.

cond-mat.stat-mech↗

arXiv2007

Melting curve and Hugoniot of molybdenum up to 400 GPa by ab initio simulations

We report ab initio calculations of the melting curve and Hugoniot of molybdenum for the pressure range 0-400 GPa, using density functional theory (DFT) in the projector augmented wave (PAW) implementation. We use the ``reference coexistence'' technique to overcome uncertainties inherent in earlier DFT calculations of the melting curve of Mo. Our calculated melting curve agrees well with experiment at ambient pressure and is consistent with shock data at high pressure, but does not agree with the high pressure melting curve from static compression experiments. Our calculated P(V) and T(P) Hugoniot relations agree well with shock measurements. We use calculations of phonon dispersion relations as a function of pressure to eliminate some possible interpretations of the solid-solid phase transition observed in shock experiments on Mo.

cond-mat.mtrl-sci↗

arXiv2006

The energetics of water on oxide surfaces by quantum Monte Carlo

Density functional theory (DFT) is widely used in surface science, but gives poor accuracy for oxide surface processes, while high-level quantum chemistry methods are hard to apply without losing basis-set quality. We argue that quantum Monte Carlo techniques allow these difficulties to be overcome, and we present diffusion Monte Carlo results for the formation energy of the MgO(001) surface and the adsorption energy of H$_2$O on this surface, using periodic slab geometry. The results agree well with experiment. We note other oxide surface problems where these techniques could yield immediate progress.

cond-mat.mtrl-sci↗

arXiv2006

Recent progress with large-scale ab initio calculations: the CONQUEST code

While the success of density functional theory (DFT) has led to its use in a wide variety of fields such as physics, chemistry, materials science and biochemistry, it has long been recognised that conventional methods are very inefficient for large complex systems, because the memory requirements scale as $N^2$ and the cpu requirements as $N^3$ (where $N$ is the number of atoms). The principles necessary to develop methods with linear scaling of the cpu and memory requirements with system size ($\mathcal{O}(N)$ methods) have been established for more than ten years, but only recently have practical codes showing this scaling for DFT started to appear. We report recent progress in the development of the \textsc{Conquest} code, which performs $\mathcal{O}(N)$ DFT calculations on parallel computers, and has a demonstrated ability to handle systems of over 10,000 atoms. The code can be run at different levels of precision, ranging from empirical tight-binding, through \textit{ab initio} tight-binding, to full \textit{ab initio}, and techniques for calculating ionic forces in a consistent way at all levels of precision will be presented. Illustrations are given of practical \textsc{Conquest} calculations in the strained Ge/Si(001) system.

cond-mat.mtrl-sci↗

arXiv2005

The Schottky defect formation energy in MgO calculated by diffusion Monte Carlo

The energetics of point defects in oxide materials plays a major role in determining their high-temperature properties, but experimental measurements are difficult, and calculations based on density functional theory (DFT) are not necessarily reliable. We report quantum Monte Carlo (QMC) calculations of the formation energy $E_{\rm S}$ of Schottky defects in MgO, which demonstrate the feasibility of using this approach to overcome the deficiencies of DFT. In order to investigate system-size errors, we also report DFT calculations of $E_{\rm S}$ on repeating cells of up to $\sim 1000$ atoms, which indicate that QMC calculations on systems of only 54 atoms should yield high precision. The DFT calculations also provide the relaxed structures used in the variational and diffusion Monte Carlo calculations. For MgO, we find $E_{\rm S}$ to be in close agreement with results from DFT and from model interaction potentials, and consistent with the scattered experimental values. The prospects for applying the same approach to transition metal oxides such as FeO are indicated.

cond-mat.mtrl-sci↗

arXiv2004

An efficient localized basis set for quantum Monte Carlo calculations on condensed matter

We present an efficient scheme for representing many-body wavefunctions in quantum Monte Carlo (QMC) calculations. The scheme is based on B-splines (blip functions), which consist of localized cubic splines centred on the points of a regular grid. We show that blip functions are unbiased, systematically improvable, and conveniently obtained from any standard plane-waves density functional theory (PW-DFT) code, and therefore provide a convenient and natural interface between PW-DFT and QMC calculations. We present tests on a 16-atom system of Si in the $β$-tin structure, and on 2- and 8- atoms systems of MgO in the NaCl structure. We show that already with such small systems the speed-up of blip functions with respect to plane-waves is between one and two order of magnitudes, without compromising the accuracy.

cond-mat.mtrl-sci↗