Time-dependent density functional theory with the orthogonal projector augmented wave method
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Nguyen, Minh [Sandia National Laboratories (SNL-NM↗
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A physics informed model for the prediction of surface energies and the shape of metal particles
Surface energies of metal-based systems are important for determining the Wulff-constructed shapes of metal nanoparticles and understanding the stability. We have developed a physics informed method to predict the total energy of metal-based systems across a wide range of configurations. Our method has been tested against density functional theory (DFT) calculations for late transition metals. This method enables on-the-fly surface energy predictions based on the fundamental of materials property and allows for the Wulff construction of metal particles for a random number of elemental atoms and without the need for DFT calculations. By making a division between atoms in the different layers of the model system, we can improve the accuracy of the model, suggesting a dissimilarity between the electronic structure due to an alternating compression and expansion of atomic layers. We find that our model accurately and effectively provides valuable insights into the distribution and stability of nanoparticles.
Mandal, Shyama Charan (ORCID:0000000245882874)↗
Improving the Accuracy of Atomistic Simulations of the Electrochemical Interface
Atomistic simulation of the electrochemical double layer is an ambitious undertaking, requiring quantum mechanical description of electrons, phase space sampling of liquid electrolytes, and equilibration of electrolytes over nanosecond time scales. All models of electrochemistry make different trade-offs in the approximation of electrons and atomic configurations, from the extremes of classical molecular dynamics of a complete interface with point-charge atoms to correlated electronic structure methods of a single electrode configuration with no dynamics or electrolyte. Here, we review the spectrum of simulation techniques suitable for electrochemistry, focusing on the key approximations and accuracy considerations for each technique. Additionally, we discuss promising approaches, such as enhanced sampling techniques for atomic configurations and computationally efficient beyond density functional theory (DFT) electronic methods, that will push electrochemical simulations beyond the present frontier.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Tuning the Redox Activity of Metal–Organic Frameworks for Enhanced, Selective O 2 Binding: Design Rules and Ambient Temperature O 2 Chemisorption in a Cobalt–Triazolate Framework
Metal–organic frameworks (MOFs) with coordinatively unsaturated metal sites are appealing as adsorbent materials due to their tunable functionality and ability to selectively bind small molecules. Through the use of computational screening methods based on periodic density functional theory, we investigate O 2 and N 2 adsorption at the coordinatively unsaturated metal sites of several MOF families. A variety of design handles are identified that can be used to modify the redox activity of the metal centers, including changing the functionalization of the linkers (replacing oxido donors with sulfido donors), anion exchange of bridging ligands (considering μ-Br – , μ-Cl – , μ-F – , μ-SH – , or μ-OH – groups), and altering the formal oxidation state of the metal. As a result, we show that it is possible to tune the O 2 affinity at the open metal sites of MOFs for applications involving the strong and/or selective binding of O 2 . In contrast with O 2 adsorption, N 2 adsorption at open metal sites is predicted to be relatively weak across the MOF dataset, with the exception of MOFs containing synthetically elusive V 2+ open metal sites. As one example from the screening study, we predicted that exchanging the μ-Cl – ligands of M 2 Cl 2 (BBTA) (H 2 BBTA = 1H,5H-benzo(1,2-d:4,5-d')bistriazole) with μ-OH – groups would significantly enhance the strength of O 2 adsorption at the open metal sites without a corresponding increase in the N 2 affinity. Experimental investigation of Co 2 Cl 2 (BBTA) and Co 2 (OH) 2 (BBTA) confirms that the former exhibits weak physisorption of both N 2 and O 2 , whereas the latter is capable of chemisorbing O 2 at room temperature in a highly selective manner. The O 2 chemisorption behavior is attributed to the greater electron-donating character of the μ-OH – ligands and the presence of H-bonding interactions between the μ-OH – bridging ligands and the reduced O 2 adsorbate.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Atom Equivalent Energies for the Rapid Estimation of the Heat of Formation of Explosive Molecules from Density Functional Tight Binding Theory
Atom equivalent energies have been derived from which the gas-phase heat of formation of explosive molecules can be estimated from fast, semiempirical density functional tight binding total energy calculations. The root-mean-square deviation and maximum deviation of the heats of formation from the experimental values for the set of 45 energetic molecules compiled by Byrd and Rice [ J. Phys. Chem. A, 2006, 110, 1005–1013] are 10.4 and 25.5 kcal/mol, respectively, using 4 atom equivalent energies and 7.4 and 15.0 kcal/mol, respectively, using 7 atom equivalent energies. These errors are around a factor of 2–3 larger than those obtained from density functional theory calculations but are smaller than those obtained from other semiempirical electronic structure methods. Heats of formation calculated with density functional tight binding theory using the 4 and 7 atom equivalent energies, the Byrd and Rice scheme, and the atom pair contribution method for a new set of 531 energetic molecules that contain only carbon, hydrogen, nitrogen, and oxygen are provided.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A framework for quantifying uncertainty in DFT energy corrections
In this work, we demonstrate a method to quantify uncertainty in corrections to density functional theory (DFT) energies based on empirical results. Such corrections are commonly used to improve the accuracy of computational enthalpies of formation, phase stability predictions, and other energy-derived properties, for example. We incorporate this method into a new DFT energy correction scheme comprising a mixture of oxidation-state and composition-dependent corrections and show that many chemical systems contain unstable polymorphs that may actually be predicted stable when uncertainty is taken into account. We then illustrate how these uncertainties can be used to estimate the probability that a compound is stable on a compositional phase diagram, thus enabling better-informed assessments of compound stability.
42 ENGINEERING↗
Nonparametric, data-based kernel interpolation for particle-tracking simulations and kernel density estimation
Traditional interpolation techniques for particle tracking include binning and convolutional formulas that use pre-determined (i.e., closed-form, parameteric) kernels. In many instances, the particles are introduced as point sources in time and space, so the cloud of particles (either in space or time) is a discrete representation of the Green’s function of an underlying PDE. As such, each particle is a sample from the Green’s function; therefore, each particle should be distributed according to the Green’s function. In short, the kernel of a convolutional interpolation of the particle sample “cloud” should be a replica of the cloud itself. This idea gives rise to an iterative method by which the form of the kernel may be discerned in the process of interpolating the Green’s function. When the Green’s function is a density, this method is broadly applicable to interpolating a kernel density estimate based on random data drawn from a single distribution. We formulate and construct the algorithm and demonstrate its ability to perform kernel density estimation of skewed and/or heavy-tailed data including breakthrough curves.
42 ENGINEERING↗
Rethinking the magnetic properties of lepidocrocite: A density functional theory and cluster expansion study
The iron oxyhydroxide lepidocrocite (g-FeOOH) is an abundant mineral critical to a number of chemical and technological applications. Of particular interest is the ground state and nite temperature magnetic order, and the subsequent impact this has upon crystal properties. The magnetic properties, investigated in this work are governed primarily through superexchange interactions, and have been calculated using density functional theory and cluster expansion methods. Quantication of these exchange terms has facilitated the determination of the ground state magneto-crystalline structure and subsequent calculation of its lattice constants, elastic moduli, cohesive enthalpy, and electronic density of states. Further, using a collinear magnetic conguration model, the magnetic heat capacity versus temperature has been studied and the Neel temperature obtained.
Pope, Daniel J.↗
Model orthogonalization and Bayesian forecast mixing via principal component analysis
One can improve predictability in the unknown domain by combining forecasts of imperfect complex computational models using a Bayesian statistical machine learning framework. In many cases, however, the models used in the mixing process are similar. In addition to contaminating the model space, the existence of such similar, or even redundant, models during the multimodeling process can result in misinterpretation of results and deterioration of predictive performance. In this paper we describe a method based on the principal component analysis that eliminates model redundancy. We show that by adding model orthogonalization to the proposed Bayesian model combination framework, one can arrive at better prediction accuracy and reach excellent uncertainty quantification performance.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Role of quadrupole deformation and continuum effects in the “island of inversion” nuclei 28,29,31 F
The peculiar properties of nuclei in the so-called “island of inversion” around Z = 10 and N = 20 are the focus of current nuclear physics research. Recent studies showed that 28 F has a negative-parity ground state and thus lies within the southern shore of the island of inversion, and 29 F presents a halo structure in its ground state, but it is unclear which effects, such as deformation, shell evolution due to tensor forces, or couplings to the continuum, lead to this situation. Here, we investigate the role of quadrupole deformation and continuum effects on the single-particle structure of 28,29,31 F from a relativistic mean-field approach and show how both phenomena can lead to a negative-parity ground state in 28 F and halo structures in 29,31 F. We solve the Dirac equation in the complex-momentum (Berggren) representation for a potential with quadrupole deformation at the first order obtained from relativistic mean-field calculations using the NL3 interaction and calculate the continuum level densities using the Green’s function method. We extract single-particle energies and widths from the continuum level densities to construct the Nilsson diagrams of 28,29,31 F in the continuum and analyze the evolution of both the widths and occupation probabilities of relevant Nilsson orbitals in 28 F and find that some amount of prolate deformation must be present. In addition, we calculate the density distributions for bound Nilsson orbitals near the Fermi surface in 29,31 F and reveal that, for a quadrupole deformation 0.3 ≤ β 2 ≤ 0.45 (prolate), characteristic halo tails appear at large distances. Using the relativistic mean-field approach in the complex-momentum representation with the Green’s function method, we demonstrate that in neutron-rich fluorine isotopes, while in the spherical case the pf shells are already inverted and close to the neutron emission threshold, a small amount of quadrupole deformation can dramatically reduce the gap between positive- and negative-parity states and increase the role of continuum states, ultimately leading to the negative parity in the ground state of 28 F and the halo structures in 29,31 F.
20 ≤ A ≤ 38↗
Unusual Exchange Couplings and Intermediate Temperature Weyl State in Co 3 Sn 2 S 2
Understanding magnetism and its possible correlations to topological properties has emerged to the forefront as a difficult topic in studying magnetic Weyl semimetals. Co 3 Sn 2 S 2 is a newly discovered magnetic Weyl semimetal with a kagome lattice of cobalt ions and has triggered intense interest for rich fantastic phenomena. In this study, we report the magnetic exchange couplings of Co 3 Sn 2 S 2 using inelastic neutron scattering and two density functional theory (DFT) based methods: constrained magnetism and multiple-scattering Green’s function methods. Co 3 Sn 2 S 2 exhibits highly anisotropic magnon dispersions and linewidths below T C , and paramagnetic excitations above T C . The spin-wave spectra in the ferromagnetic ground state is well described by the dominant third-neighbor “across-hexagon” J d model. Our density functional theory calculations reveal that both the symmetry-allowed 120° antiferromagnetic orders support Weyl points in the intermediate temperature region, with distinct numbers and the locations of Weyl points. Our study highlights the important role Co 3 Sn 2 S 2 can play in advancing our understanding of kagome physics and exploring the interplay between magnetism and band topology.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Algorithm advances and applications of time‐dependent first‐principles simulations for ultrafast dynamics
Abstract Far from equilibrium phenomenon is a central theme of contemporary material research. Such phenomenon can exhibit itself in atomic structure and dynamics, but very often it also happens as non‐equilibrium phenomenon in the electronic structure. In ab initio material simulation, density functional theory (DFT) has played an essential role in studying electronic ground state problems. For excited states, besides many‐body perturbation theory, another powerful tool is the time dependent DFT (TDDFT) method. In particular, the real‐time TDDFT (rt‐TDDFT) method can be used to simulate many non‐equilibrium phenomena directly. Here we introduce our works on some algorithm advances based on our recently rt‐TDDFT method. This method uses the plane‐wave basis set, and significantly accelerates its efficiency by increasing the time step from 0.1–1 as in traditional methods to 0.2–0.5 fs. The noncollinear magnetic moments and spin–orbit coupling have also been included in our rt‐TDDFT method. Furthermore, a Boltzmann‐TDDFT algorithm has been developed to solve the hot carrier overheating problem in Ehrenfest dynamics, and a natural orbital branching algorithm has been developed to overcome the mean‐field approximation in Ehrenfest dynamics nuclear trajectory, thus allows stochastic multiple paths in chemical reactions. Utilizing these methods, we have studied the photoinduced ultrafast demagnetization, ultrafast phase transition, energy transfer between plasmon and hot carriers, as well as the high‐energy ion implantation and low‐energy atomic diffusion in semiconductors. We believe the tools as the ones introduced here can enable us to study a wide range of phenomena which are of great interest in modern day material research. This article is categorized under: Structure and Mechanism > Computational Materials Science Electronic Structure Theory > Ab Initio Electronic Structure Methods Electronic Structure Theory > Density Functional Theory
Liu, Wen‐Hao↗
First-principles predictions of temperature-dependent infrared dielectric function of polar materials by including four-phonon scattering and phonon frequency shift
Recently, first-principles calculations based on density functional theory have been widely used to predict the temperature-dependent infrared spectrum of polar materials, but the calculations are usually limited to the harmonic frequency (0 K) and three-phonon scattering damping for the zone-center infrared-active optical phonon modes, and fail to predict the high-temperature infrared optical properties of materials such as sapphire (α–Al 2 O 3 ), GaAs, TiO 2 , etc., due to the neglect of high-order phonon scattering damping and phonon frequency shift. In this work, we implemented first-principles calculations to predict the temperature-dependent infrared dielectric function of polar materials by including four-phonon scattering and phonon frequency shift. The temperature-dependent phonon damping by including three- and four-phonon scattering as well as the phonon frequency shift by including cubic and quartic anharmonicity and the thermal expansion effect are calculated based on anharmonic lattice dynamics method. The infrared dielectric function of α–Al 2 O 3 is parameterized, and then the temperature-dependent infrared optical reflectance is determined. We find that our predictions agree better with the experimental data than the previous density functional theory-based methods. Lastly, this work will help to effectively predict the thermal radiative properties of polar materials at elevated temperature, which is generally difficult to measure, and will enable predictive design of new materials for radiative applications.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Static Subspace Approximation for Random Phase Approximation Correlation Energies: Implementation and Performance
Developing theoretical understanding of complex reactions and processes at interfaces requires using methods that go beyond semilocal density functional theory to accurately describe the interactions between solvent, reactants and substrates. Methods based on many-body perturbation theory, such as the random phase approximation (RPA), have previously been limited due to their computational complexity. However, this is now a surmountable barrier due to the advances in computational power available, in particular through modern GPU-based supercomputers. In this work, we describe the implementation of RPA calculations within BerkeleyGW and show its favorable computational performance on large complex systems relevant for catalysis and electrochemistry applications. Our implementation builds off of the static subspace approximation which, by employing a compressed representation of the frequency dependent polarizability, enables the evaluation of the RPA correlation energy with significant acceleration and systematically controllable accuracy. We find that the computational cost of calculating the RPA correlation energy scales only linearly with system size for systems containing up to 50 thousand bands, and is expected to scale quadratically thereafter. We also show excellent strong scaling results across several supercomputers, demonstrating the performance and portability of this implementation.
algorithmic development↗
Toward Quantum Chemical Free Energy Simulations of Platinum Nanoparticles on Titania Support
Platinum nanoparticles (Pt-NPs) supported on titania surfaces are costly but indispensable heterogeneous catalysts because of their highly effective and selective catalytic properties. Therefore, it is vital to understand their physicochemical processes during catalysis to optimize their use and to further develop better catalysts. However, simulating these dynamic processes is challenging due to the need for a reliable quantum chemical method to describe chemical bond breaking and bond formation during the processes but, at the same time, fast enough to sample a large number of configurations required to compute the corresponding free energy surfaces. Density functional theory (DFT) is often used to explore Pt-NPs; nonetheless, it is usually limited to some minimum-energy reaction pathways on static potential energy surfaces because of its high computational cost. In this work, we report a combination of the density functional tight binding (DFTB) method as a fast but reliable approximation to DFT, the steered molecular dynamics (SMD) technique, and the Jarzynski equality to construct free energy surfaces of the temperature-dependent diffusion and growth of platinum particles on a titania surface. In particular, we present the parametrization for Pt-X (X = Pt, Ti, or O) interactions in the framework of the second-order DFTB method, using a previous parametrization for titania as a basis. The optimized parameter set was used to simulate the surface diffusion of a single platinum atom (Pt 1 ) and the growth of Pt 6 from Pt 5 and Pt 1 on the rutile (110) surface at three different temperatures (T = 400, 600, 800 K). The free energy profile was constructed by using over a hundred SMD trajectories for each process. We found that increasing the temperature has a minimal effect on the formation free energy; nevertheless, it significantly reduces the free energy barrier of Pt atom migration on the TiO 2 surface and the transition state (TS) of its deposition. In a concluding remark, the methodology opens the pathway to quantum chemical free energy simulations of Pt-NPs’ temperature-dependent growth and other transformation processes on the titania support.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Relativistic density functional theory in the full potential linear muffin tin orbital method
In this write-up, we have outlined the general methodology for treating relativity in the FP-LMTO method. The Schrodinger equation is insufficient for describing the physics of heavy elements because it leaves out any relativistic effects. Therefore DFT based on the Schrodinger equation is not sufficient for studying heavy materials. It is, however, possible to incorporate all of the effects of relativity in DFT if starting with a reformulation of the Hohenberg-Kohn theorem that proceeds from the Dirac equation, rather than the Schrodinger equation. The corresponding theorem in relativistic density functional theory (RDFT) shows that the ground-state density of the system is a functional of not only the charge density as in Schrodinger-based DFT, but also of the current density. This leads to a more elaborate procedure in practice when solving the Dirac-Kohn-Sham equations, the relativistic analogs of the Kohn-Sham equations.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Protein Molecular Dynamics Simulations with Approximate QM: What Can We Learn?
Classical force fields are essential for computer simulations of proteins and are typically parameterized to reproduce secondary and tertiary structure of isolated proteins. However, while protein-protein interactions are ubiquitous in nature, they are not considered in parameterization efforts and are far less understood than isolated proteins. A better characterization of intermolecular interactions is widely recognized as a key to revolutionizing drug and therapeutic developments with high-throughput computational screening. Urgently needed is a critical assessment of the performance of modern protein force fields against first-principles electronic structure methods and experiments. In a daring step toward this goal, we here describe a comparison of peptide folding dynamics as predicted by a molecular mechanics force field on the one hand and by an approximate electronic structure quantum mechanical (QM) method based on density-functional tight-binding (DFTB) on the other. We further compare the dynamics from straightforward DFTB simulations with a near-linear scaling version of DFTB for massively parallel computation based on the fragment molecular orbital (FMO-DFTB) method. We illustrate differences between the phenomenology of the folding dynamics from these three methods for a small model peptide, as well as charge polarization and dynamic fluctuations, point out possible correlations and implications for force field developers, and discuss the lessons learned that might become applicable to future predictive high-throughput computer screening for personalized neoantigen cancer therapy.
Irle, Stephan↗