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 Mo{}ller-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.

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.

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.

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.

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.

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.

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.

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.

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.

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.