We present in detail the recently derived ab-initio molecular dynamics (AIMD) formalism [Phys. Rev. Lett. 101 096403 (2008)], which due to its numerical properties, is ideal for simulating the dynamics of systems containing thousands of atoms. A major drawback of traditional AIMD methods is the necessity to enforce the orthogonalization of the wave-functions, which can become the bottleneck for very large systems. Alternatively, one can handle the electron-ion dynamics within the Ehrenfest scheme where no explicit orthogonalization is necessary, however the time step is too small for practical applications. Here we preserve the desirable properties of Ehrenfest in a new scheme that allows for a considerable increase of the time step while keeping the system close to the Born-Oppenheimer surface. We show that the automatically enforced orthogonalization is of fundamental importance for large systems because not only it improves the scaling of the approach with the system size but it also allows for an additional very efficient parallelization level. In this work we provide the formal details of the new method, describe its implementation and present some applications to some test systems. Comparisons with the widely used Car-Parrinello molecular dynamics method are made, showing that the new approach is advantageous above a certain number of atoms in the system. The method is not tied to a particular wave-function representation, making it suitable for inclusion in any AIMD software package.
A new "on the fly" method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic orbitals are evolved by a Schroedinger-like equation, where the orbital time derivative is multiplied by a parameter. This parameter controls the time scale of the fictitious electronic motion and speeds up the calculations with respect to standard Ehrenfest dynamics. In contrast to other methods, wave function orthogonality needs not be imposed as it is automatically preserved, which is of paramount r…
The atomistic resolution recently achieved by ultrafast spectroscopies demands corresponding theoretical advances. Real-time time-dependent density-functional theory (RT-TDDFT) with Ehrenfest dynamics offers an optimal trade-off between accuracy and computational costs to study electronic and vibrational dynamics of laser-excited materials in the sub-picosecond regime. However, this approach is unable to account for thermal effects or zero-point energies which are crucial in the physics involved. Herein, we adopt a quantum-semiclassical method based on RT-TDDFT+Ehrenfest to simulate laser-indu…
We have derived equations for nonadiabatic Ehrenfest molecular dynamics which conserve the total energy in the case of time-dependent discretization for electrons. A discretization is time-dependent in all cases where it or part of it depends on the positions of the nuclei, for example, in atomic orbital basis sets, and in the projector augmented-wave (PAW) method, where the augmentation functions depend on the nuclear positions. We have derived, implemented, and analyzed the energy conserving equations and their most common approximations for a 1D test system where we can achieve numerical re…
The relation between ab initio molecular dynamics formalism and the electron-phonon interaction formalism [P.B. Allen and V. Heine, J. Phys. C 9, 2305 (1976)] is explored. The fundamental quantity obtained in the AIMD formalism - total energy for any configuration - is also obtained from the formalism (ES-DWF) that incorporates the role of Debye-Waller Factor in electronic structure calculations. The two formalisms are exactly equivalent and represent the direct and perturbation theory approaches to determine total energy. This equivalence allows either formalism to be used depending on the re…
Nonradiative carrier recombination is of both great applied and fundamental importance.But the correct ab initio approaches to calculate it remains to be inconclusive. Here we used 5 different formalisms to calculate the nonradiative carrier recombinations of two complex defect structures GaP:Zn_Ga-O_P and GaN:Zn_Ga-V_N, and compared the results with experiments.In order to apply different multiphonon assisted electron transition formalisms, we have calculated the electron-phonon coupling constants by ab initio density functional theory for all phonon modes. Compared with different methods, th…
In materials with strong electron-phonon (e-ph) interactions, charge carriers can distort the surrounding lattice and become trapped, forming self-localized (small) polarons. We recently developed an ab initio approach based on canonical transformations to efficiently compute the formation and energetics of small polarons[1]. A different approach based on a Landau-Pekar energy functional has been proposed in the recent literature [2,3]. In this work, we analyze and compare these two methods in detail. We show that the small polaron energy is identical in the two formalisms when using the same …
We present a combined treatment of the non-equilibrium dynamics and transport of electrons and phonons by carrying out \textit{ab initio} calculations of the fully coupled electron and phonon Boltzmann transport equations. We find that the presence of mutual drag between the two carriers causes the thermopower to be enhanced and dominated by the transport of phonons, rather than electrons as in the traditional semiconductor picture. Drag also strongly boosts the intrinsic electron mobility, thermal conductivity and the Lorenz number. Impurity scattering is seen to suppress the drag-enhancement…
In this paper, we show how to calculate analytical atomic forces within self-consistent density functional theory + dynamical mean-field theory (DFT+DMFT) approach in the case when ultra-soft or norm-conserving pseudopotentials are used. We show how to treat the non-local projection terms arising within the pseudopotential formalism and circumvent the problem of non-orthogonality of the Kohn-Sham eigenvectors. Our approach is, in principle, independent of the DMFT solver employed, and here was tested with the Hubbard I solver. We benchmark our formalism by comparing against the forces calculat…
A Kubo-Greenwood-like equation for the Gilbert damping parameter $α$ is presented that is based on the linear response formalism. Its implementation using the fully relativistic Korringa-Kohn-Rostoker (KKR) band structure method in combination with Coherent Potential Approximation (CPA) alloy theory allows it to be applied to a wide range of situations. This is demonstrated with results obtained for the bcc alloy system Fe$_x$Co$_{1-x}$ as well as for a series of alloys of permalloy with 5d transition metals. To account for the thermal displacements of atoms as a scattering mechanism, an alloy…
We develop a formalism for the evaluation of conduction eigenchannels of atomic-sized contacts from first-principles. The multiple scattering Korringa-Kohn-Rostoker (KKR) Green's function method is combined with the Kubo linear response theory. Solutions of the eigenvalue problem for the transmission matrix are proven to be identical to eigenchannels introduced by Landauer and B{ü}ttiker. Applications of the method are presented by studying ballistic electron transport through Cu, Pd, Ni and Co single-atom contacts. We show in detail how the eigenchannels are classified in terms of irreducible…
In this paper we derive a formalism allowing us to separate inter-layer contributions to the polarizability of a periodic array of 2D materials from intra-layer ones. To this aim, effective profile functions are introduced. They constitute a tight-binding-like layer-localized basis involving two lengths, the effective thickness $d$ characteristic of the 2D material and the inter-layer separation $L$. The method permits, within the same formalism, either to compute the single-layer dielectric function from an ab-initio periodic calculation (top-down strategy) or to stack several 2D materials to…
We benchmark a set of quantum-chemistry methods, including multitrajectory Ehrenfest, fewest-switches surface-hopping, and multiconfigurational-Ehrenfest dynamics, against exact quantum-many-body techniques by studying real-time dynamics in the Holstein model. This is a paradigmatic model in condensed matter theory incorporating a local coupling of electrons to Einstein phonons. For the two-site and three-site Holstein model, we discuss the exact and quantum-chemistry methods in terms of the Born-Huang formalism, covering different initial states, which either start on a single Born-Oppenheime…
{\it Ab initio\} calculations have been successfully used for evaluating lattice dynamical properties of solids within the (quasi-)harmonic approximation (i.e., assuming non-interacting phonons with infinite lifetimes), but it remains difficult to treat anharmonicity in all but the simplest compounds. We detail a systematic information theory based approach to deriving {\it ab initio\} anharmonic force constants: compressive sensing lattice dynamics (CSLD). The non-negligible terms that are necessary to reproduce the first-principles calculated interatomic forces are automatically selected by …
Thermal vibrations alter the external potential. Allen (Phys. Rev. B 18 (1978) 5217) proved that at finite temperatures the pseudopotential form factors are corrected by a Debye-Waller Factor (DWF). We generalize this result to the crystal potential. (The generalization to the all-electron case of the nuclear potential fails due to the breakdown of the rigid-atom approximation.) This finite temperature formalism only gives thermal-averaged properties and no dynamical information can be obtained. Hence, it is labeled the Quasi Ab Initio formalism. Analogous to the use of experimental lattice pa…
We develop an ab initio formalism for dipolar electron-phonon interactions (EPI) in two-dimensional (2D) materials. Unlike purely longitudinal Fröhlich model, we show that the out-of-plane dipoles also contribute to the long-wavelength non-analytical behavior of EPI. And the 2D dipolar EPI plays an important role not only in the typical polar material MoS$_2$, but also in graphane and fluorinated graphene. By incorporating this formalism into Wannier-Fourier interpolation, we enable accurate EPI calculations for 2D materials and subsequent intrinsic carrier mobility prediction. The results sho…
We develop a theoretical and computational framework to study polarons in semiconductors and insulators from first principles. Our approach provides the formation energy, excitation energy, and wavefunction of both electron and hole polarons, and takes into account the coupling of the electron or hole to all phonons. An important feature of the present method is that it does not require supercell calculations, and relies exclusively on electron band structures, phonon dispersions, and electron-phonon matrix elements obtained from calculations in the crystal unit cell. Starting from the Kohn-Sh…
Using the Green's function formalism, an ab initio theory for band structures of crystals is derived starting from the Hartree-Fock approximation. It is based on the algebraic diagrammatic construction scheme for the self-energy which is formulated for crystal orbitals (CO-ADC). In this approach, the poles of the Green's function are determined by solving a suitable Hermitian eigenvalue problem. The method is not only applicable to the outer valence and conduction bands, it is also stable for inner valence bands where strong electron correlations are effective. The key to the proposed scheme i…
A recently developed linear-scaling density-functional theory (LS-DFT) formalism is used to calculate optical absorption spectra of hybrids of C60 and the conjugated polymers poly(para-phenylene) (PPP) and poly(para-phenylene vinylene) (PPV). The use of a LS formalism allows calculations on large systems with realistic proportions of C60, which has been of interest for the use of such materials in photovoltaics. Two different bonding structures are tested for the hybrid PPP and for both systems additional peaks are present in the absorption spectra below the original onset of absorption. By id…
We describe our theoretical formalism and computational scheme for making ab-initio calculations of the dynamic paramagnetic spin susceptibilities of metals and alloys at finite temperatures. Its basis is Time-Dependent Density Functional Theory within an electronic multiple scattering, imaginary time Green function formalism. Results receive a natural interpretation in terms of overdamped oscillator systems making them suitable for incorporation into spin fluctuation theories. For illustration we apply our method to the nearly ferromagnetic metal Pd and the nearly antiferromagnetic chromium a…
We present a novel ab initio non-equilibrium approach to calculate the current across a molecular junction. The method rests on a wave function based full ab initio description of the central region of the junction combined with a tight binding approximation for the electrodes in the frame of the Keldysh Green's function formalism. Our procedure is demonstrated for a dithiolethine molecule between silver electrodes. The main conducting channel is identified and the full current-voltage characteristic is calculated.
We present a novel technique for calculating the dielectric response of metal/insulator heterostructures. This scheme allows, for the first time, the fully first-principles calculation of the microscopic properties of thin-film capacitors at finite bias potential. The method can be readily applied to pure insulators, where it provides an interesting alternative to conventional finite-field techniques based on the Berry-phase formalism. We demonstrate the effectiveness of our method by performing comprehensive numerical tests on a model Ag/MgO/Ag heterostructure.
We present a theoretical framework to describe polarons from first principles within a many-body Green's function formalism. Starting from a general electron-phonon Hamiltonian, we derive a self-consistent Dyson equation in which the phonon-mediated self-energy is composed by two distinct terms. One term is the Fan-Migdal self-energy and describes dynamic electron-phonon processes, the other term is a new contribution to the self-energy originating from the static displacements of the atomic nuclei in the polaronic ground state. The lowest-order approximation to the present theory yields the s…
We present a novel ab initio non-equilibrium approach to calculate the current across a molecular junction. The method rests on a wave function based description of the central region of the junction combined with a tight binding approximation for the electrodes in the frame of the Keldysh Green's function formalism. In addition we present an extension so as to include effects of the two-particle propagator. Our procedure is demonstrated for a dithiolbenzene molecule between silver electrodes. The full current-voltage characteristic is calculated. Specific conclusions for the contribution of c…
We report first principles analysis of electron-phonon coupling in molecular devices under external bias voltage and during current flow. Our theory and computational framework are based carrying out density functional theory within the Keldysh nonequilibrium Green's function formalism. We analyze which molecular vibrational modes are most relevant to charge transport under nonequilibrium conditions. For a molecular tunnel junction of a 1,4-benzenedithiolate molecule contacted by two leads, the low-lying modes of the vibration are found to be most important. As a function of bias voltage, the …
We present an ab-initio study of the electronic response function of sodium in its 5 known metallic phases from 0 to 180 GPa at room temperature. The considered formalism is based on a interpolation scheme within time-dependent density functional theory that uses maximally localized Wannier functions, providing an accurate sampling of the reciprocal space. Besides showing an excellent agreement with inelastic X-ray scattering experiments, our calculations reveal that the drastic decrease of the optical reflectivity recently measured in the high pressure phases oP8 and tI19 is associated to a n…
We develop a method for calculating the electron-phonon vertex in polar semiconductors and insulators from first principles. The present formalism generalizes the Fröhlich vertex to the case of anisotropic materials and multiple phonon branches, and can be used either as a post-processing correction to standard electron-phonon calculations, or in conjunction with {\it ab initio} interpolation based on maximally localized Wannier functions. We demonstrate this formalism by investigating the electron-phonon interactions in anatase TiO$_2$, and show that the polar vertex significantly reduces the…
We present a method to microscopically derive a small-size k$\cdot$p Hamiltonian in a Hilbert space spanned by physically chosen ab initio spinor wave functions. Without imposing any complementary symmetry constraints, our formalism equally treats three- and two-dimensional systems and simultaneously yields the Hamiltonian parameters and the true $\mathbb{Z}_2$ topological invariant. We consider bulk crystals and thin films of Bi$_{2}$Se$_{3}$, Bi$_{2}$Te$_{3}$, and Sb$_{2}$Te$_{3}$. It turns out that the effective continuous k$\cdot$p models with open boundary conditions often incorrectly pre…
We report calculated, electronic and related properties of wurtzite and zinc blende gallium nitrides (w-GaN, zb-GaN). We employed a local density approximation (LDA) potential and the linear combination of atomic orbital (LCAO) formalism. The implementation of this formalism followed the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). The calculated electronic and related properties, for both structures of GaN, are in good agreement with corresponding, experimental data, unlike results from most previous ab initio calculations utilizing a density function…
By carrying out density functional theory (DFT) analysis within the Keldysh non-equilibrium Green's function (NEGF) framework, we investigate the quantum transport properties of Au-C60-Au molecular junctions from the first principles. We briefly review the NEGF-DFT formalism and present some of our data. We found that at small electrode separations (9-13 Angstrom), the Au-C60-Au junctions show metallic behaviour with conductance G ~ 2e^{2}/h and current I ~ 1-3 microAmpere in the linear regime (bias voltage V < 0.3 Volt). The physical mechanism is the resonance tunnelling through partially occ…
Transport properties of permalloy doped with V, Co, Pt, and Au are explored via ab-initio calculations. The Kubo-Bastin formula is evaluated within the fully relativistic Korringa-Kohn-Rostoker Green function formalism. Finite temperature effects are treated by means of the alloy analogy model. It is shown that the fact that the host is disordered and not crystalline has a profound effect on how the conductivities characterizing the anomalous Hall effect and the spin Hall effect depend on the dopant concentration. Several relationships between quantities characterizing charge and spin transpor…
A combination of ab initio simulations and linear-scaling Green's functions techniques is used to analyze the transport properties of long (up to one micron) carbon nanotubes with realistic disorder. The energetics and the influence of single defects (mono- and di-vacancies) on the electronic and transport properties of single-walled armchair carbon nanotubes are analyzed as a function of the tube diameter by means of the local orbital first-principles Fireball code. Efficient O(N) Green's functions techniques framed within the Landauer-Buttiker formalism allow a statistical study of the nanot…
The quasiparticle interference (QPI) technique is a powerful tool that allows to uncover the structure and properties of electronic structure of a material combined with scattering properties of defects at surfaces. Recently this technique has been pivotal in proving the unique properties of the surface state of topological insulators which manifests itself in the absence of backscattering. In this work we derive a Green function based formalism for the ab initio computation of Fourier-transformed QPI images. We show the efficiency of our new implementation at the examples of QPI that forms ar…
We formulate a first-principle scheme for structural optimization at finite temperature ($T$) based on the self-consistent phonon (SCP) theory, which accurately takes into account the effect of strong phonon anharmonicity. The $T$-dependence of the shape of the unit cell and internal atomic configuration is determined by minimizing the variational free energy in the SCP theory. At each optimization step, the interatomic force constants in the new structure are calculated without running additional electronic structure calculations, which makes the method dramatically efficient. We demonstrate …
We study the temperature dependent dynamical processes of a Si10H16 cluster and obtain a blue shift of the Si-Si vibrational modes with transverse acoustic character and a red shift of the other vibrational modes with increasing temperature. We link this behavior to the bond length expansion and the varying sign of the Grueneisen parameter. We further present a computational approach able to extract the vibron-vibron coupling strength in clusters or molecules. Our approach is based on ab initio Born-Oppenheimer molecular dynamics and a projection formalism able to deliver the individual vibron…
We present a generalized definition of subspace occupancy matrices in ab initio methods for strongly correlated materials, such as DFT+U and DFT+DMFT, which is appropriate to the case of nonorthogonal projector functions. By enforcing the tensorial consistency of all matrix operations, we are led to a subspace projection operator for which the occupancy matrix is tensorial and accumulates only contributions which are local to the correlated subspace at hand. For DFT+U in particular, the resulting contributions to the potential and ionic forces are automatically Hermitian, without resort to sym…
We present an ab initio theory of the Gilbert damping in substitutionally disordered ferromagnetic alloys. The theory rests on introduced nonlocal torques which replace traditional local torque operators in the well-known torque-correlation formula and which can be formulated within the atomic-sphere approximation. The formalism is sketched in a simple tight-binding model and worked out in detail in the relativistic tight-binding linear muffin-tin orbital (TB-LMTO) method and the coherent potential approximation (CPA). The resulting nonlocal torques are represented by nonrandom, non-site-diago…
We present results of a study of small stoichiometric $Cd_{n}Te_{n}$ ($1{\leq}n{\leq}6$) clusters and few medium sized non-stoichiometric $Cd_{m}Te_{n}$ [($m,n= 13, 16, 19$); ($m{\neq}n$)] clusters using the Density Functional formalism and projector augmented wave method within the generalized gradient approximation. Structural properties {\it viz.} geometry, bond length, symmetry and electronic properties like HOMO-LUMO gap, binding energy, ionization potential and nature of bonding {\it etc.} have been analyzed. Medium sized non-stoichiometric clusters were considered as fragments of the bu…
We introduce a simple scheme to efficiently compute photon exchange-correlation contributions due to the coupling to transversal photons as formulated in the newly developed quantum-electrodynamical density functional theory (QEDFT). Our construction employs the optimized-effective potential (OEP) approach by means of the Sternheimer equation to avoid the explicit calculation of unoccupied states. We demonstrate the efficiency of the scheme by applying it to an exactly solvable GaAs quantum ring model system, a single azulene molecule, and chains of sodium dimers, all located in optical caviti…
We present an ab initio theory of the spin-wave stiffness tensor for ordered and disordered itinerant ferromagnets with pair exchange interactions derived from a method of infinitesimal spin rotations. The resulting formula bears an explicit form of a linear-response coefficient which involves one-particle Green's functions and effective velocity operators encountered in a recent theory of electron transport. Application of this approach to ideal metal crystals yields more reliable values of the spin stiffness than traditional ill-convergent real-space lattice summations. The formalism can als…
The elastic, thermodynamic, electronic, and optical properties of recently discovered and potentially technologically important transition metal boride NbRuB, have been investigated using the density functional formalism. Both generalized gradient approximation (GGA) and local density approximation (LDA) were used for geometrical optimization and for estimation of various elastic moduli and constants. The optical properties of NbRuB have been studied for the first time with different photon polarizations. The frequency (energy) dependences of various optical constants compliment quite well to …
We present an ab-initio formalism for the calculation of transport properties in compositionally disordered systems within the framework of the Korringa-Kohn-Rostoker non-local coherent potential approximation. Our formalism is based upon the single-particle Kubo-Greenwood linear response and provides a natural means of incorporating the effects of short-range order upon the transport properties. We demonstrate the efficacy of the formalism by examining the effects of short-range order and clustering upon the transport properties of disordered $AgPd$ and $CuZn$ alloys.
