Ab Initio Molecular Dynamics Method Research Articles

Collective modes in liquid binary alloys. An ab initio molecular dynamics study of theLiMg and LiBa alloys

We report a study on several structural and dynamical properties of the liquid Li–Mg andLi–Ba alloys. The study has been carried out by means of the orbital free ab initiomolecular dynamics method, combined with local ionic pseudopotentials constructedwithin the same framework. The results show good agreement with the availableexperimental data, accounting fairly well for the different ordering tendenciesexhibited by these alloys. We analyse the dependence of the longitudinal andtransverse collective modes on the concentration and the mass ratio of the alloy,with the latter ranging from to .

Efficient Quantum Monte Carlo Energies for Molecular Dynamics Simulations

A method is presented to treat electrons within the many-body quantum Monte Carlo (QMC) approach "on-the-fly" throughout a molecular dynamics (MD) simulation. Our approach leverages the large (10-100) ratio of the QMC electron to MD ion motion to couple the stochastic, imaginary-time electronic and real-time ionic trajectories. This continuous evolution of the QMC electrons results in highly accurate total energies for the full dynamical trajectory at a fraction of the cost of conventional, discrete sampling. We show that this can be achieved efficiently for both ground and excited states with only a modest overhead to an ab initio MD method. The accuracy of this dynamical QMC approach is demonstrated for a variety of systems, phases, and properties, including optical gaps of hot silicon quantum dots, dissociation energy of a single water molecule, and heat of vaporization of liquid water.

The effect of temperature on the seismic anisotropy of the perovskite and post-perovskite polymorphs of MgSiO3

Using elastic constants determined by ab initio molecular dynamics over a range of temperatures, we show that the seismic anisotropy of MgSiO3 perovskite is significantly temperature dependent. At 90 GPa, the direction of greatest shear wave splitting changes from [001] at 0 K to [010] at 3500 K. In addition, there is no shear wave splitting in the [100] direction at 0 K, but a significant amount of splitting is exhibited at 3500 K. We have also calculated the first set of high-temperature elastic constants of the new post-perovskite phase by ab initio molecular dynamics methods. We find that, in contrast to MgSiO3 perovskite, temperature has little effect on the acoustic anisotropy of this phase. We determine ∂ln VS/∂ln VP for the post-perovskite phase and find it to be very low, about 0.9. This may be an important parameter for mapping out the post-perovskite phase in the lowermost mantle.

Optimizing the Structures of Minimum and Transition State on the Free Energy Surface

Presented here is the application of a scheme for optimizing the structures of minima and transition states on the free energy surface (FES) for a path along a fixed reaction coordinate with the aid of ab initio molecular dynamics (AIMD) simulation. In the direction of the reaction coordinate, the values corresponding to the stationary points were optimized using the quasi-Newton method, in which the gradient of the free energy along the reaction coordinate was obtained by a constraint AIMD method, and the Bofill Hessian update scheme was used. The equilibrium values for the other directions were taken as the corresponding averages in the dynamic simulation. This scheme was applied to several elementary bimolecular addition reactions: (A) BH(3) + H(2)O --> H(2)O.BH(3); (B) BF(3) + NH(3) --> FB(3).NH(3); (C) SO(3) + NH(3) --> O(3)S.NH(3); (D) C(2)H(4) + CCl(2) --> H(4)C(2).CCl(2); (E) Ni(NH(2))(2) + PH(3) --> (NH(2))(2)Ni.PH(3); (F) W(CO)(5) + CO --> W(CO)(6). For reactions A, B, C, and F, no transition state (TS) exists on the potential energy surface (PES). However there is a TS on the FES. This stems from the curvature difference of the PES and -TDeltaS as a function of the reaction coordinate. For all reactions, it is found that the TS shifts toward the complexation product with increasing temperature because of the curvature increase of -TDeltaS. The equilibrium bond distances for the inactive coordinates perpendicular to the reaction coordinate always increase with temperature, which is due to the thermal excitation and anharmonicity of the PES.

Density functional calculation of the electronic absorption spectrum of Cu+ and Ag+ aqua ions

The UV absorption of aqueous Cu+ and Ag+ has been studied using Time Dependent Density Functional Theory (TDDFT) response techniques. The TDDFT electronic spectrum was computed from finite temperature dynamical trajectories in solution generated using the Density Functional Theory (DFT) based Ab Initio Molecular Dynamics (AIMD) method. The absorption of the two ions is shown to arise from similar excitation mechanisms, namely transitions from d orbitals localized on the metal center to a rather delocalized state originating from hybridization of the metal s orbital to the conduction band edge of the solvent. The ions differ in the way the spectral profile builds up as a consequence of solvent thermal motion. The Cu+ absorption is widely modulated, both in transition energies and intensities by fluctuations in the coordination environment which is characterized by the formation of strong coordination bonds to two water molecules in an approximately linear geometry. Though, on average, absorption intensities are typical of symmetry forbidden transitions of metal ions in the solid state, occasionally very short (<100 fs) bursts in intensity are observed, associated with anomalous Cu-H interactions. Absorption by the Ag+ complex is in comparison relatively stable in time, and can be interpreted in terms of the energy splitting of the metal 4d manifold in an average crystal field corresponding to a fourfold coordination in a distorted tetrahedral arrangement. Whereas the spectral profile of the Ag+ aqua ion is in good agreement with experiment, the overall position of the band is underestimated by 2 eV in the BLYP approximation to DFT. The discrepancy with experiment is reduced to 1.3 eV when a hybrid functional (PBE0) is used. The remaining inaccuracy of TDDFT in this situation is related to the delocalized character of the target state in d-->s transitions.

Scalable fine-grained parallelization of plane-wave-based ab initio molecular dynamics for large supercomputers.

Many systems of great importance in material science, chemistry, solid-state physics, and biophysics require forces generated from an electronic structure calculation, as opposed to an empirically derived force law to describe their properties adequately. The use of such forces as input to Newton's equations of motion forms the basis of the ab initio molecular dynamics method, which is able to treat the dynamics of chemical bond-breaking and -forming events. However, a very large number of electronic structure calculations must be performed to compute an ab initio molecular dynamics trajectory, making the efficiency as well as the accuracy of the electronic structure representation critical issues. One efficient and accurate electronic structure method is the generalized gradient approximation to the Kohn-Sham density functional theory implemented using a plane-wave basis set and atomic pseudopotentials. The marriage of the gradient-corrected density functional approach with molecular dynamics, as pioneered by Car and Parrinello (R. Car and M. Parrinello, Phys Rev Lett 1985, 55, 2471), has been demonstrated to be capable of elucidating the atomic scale structure and dynamics underlying many complex systems at finite temperature. However, despite the relative efficiency of this approach, it has not been possible to obtain parallel scaling of the technique beyond several hundred processors on moderately sized systems using standard approaches. Consequently, the time scales that can be accessed and the degree of phase space sampling are severely limited. To take advantage of next generation computer platforms with thousands of processors such as IBM's BlueGene, a novel scalable parallelization strategy for Car-Parrinello molecular dynamics is developed using the concept of processor virtualization as embodied by the Charm++ parallel programming system. Charm++ allows the diverse elements of a Car-Parrinello molecular dynamics calculation to be interleaved with low latency such that unprecedented scaling is achieved. As a benchmark, a system of 32 water molecules, a common system size employed in the study of the aqueous solvation and chemistry of small molecules, is shown to scale on more than 1500 processors, which is impossible to achieve using standard approaches. This degree of parallel scaling is expected to open new opportunities for scientific inquiry.

Interconversion behavior of the C-H bond in the CH4+ radical cation: ab initio molecular dynamics study.

Thermal motion of CH4+ is investigated by performing an ab initio molecular dynamics method with the second-order Møller-Plesset (MP2)/6-311G** force field. In the trajectories obtained at 400 K, we have observed rapid interconversion behavior of the geometrical parameters of CH4+ with the frequency of 0.6/ps, where the C-H pair forming the small angle around 55 degrees is switched to another pair on subpicosecond time scale. The switching patterns are found to be classified into the following two types. Type 1: one C-H of the small angled C-H pair is switched to one C-H of the other C-H pair. Type 2: the small angled C-H pair is switched to the other C-H pair, which has been newly observed in the present ab initio MD calculation. The four C-H bonds of CH4+ are characterized by the long and short C-H bonds in a time region of the trajectories, and also for the time-evolution of C-H bonds such interconversion behavior is observed. The switching patterns of the geometrical parameters are compared with those in the interconversion scheme between six equivalent C2v symmetry structures of CH4+ [Paddon-Row, M. N. et al., J Am Chem Soc 1985, 107, 7696]. We have also investigated the electronic energy fluctuation due to thermal motion of CH4+. The standard deviation of total electronic energy at 400 K is evaluated to be 1.2 kcal/mol.

Direct ab initio molecular dynamics study of the two photodissociation channels of formic acid

A total of ∼1200 trajectories have been integrated for the two photodissociation channels of formic acid, HCOOH → H2O + CO (1) and HCOOH → CO2 + H2 (2), which occur with 248 and 193 nm photons, using the direct ab initio molecular dynamics method at the RMP2(full)/cc-pVDZ level of theory. It was found that the percentage of the energy distributed to a relative translational mode in reaction (2) is much larger than that in reaction (1). This is mainly due to the difference in the geometry of transition state (TS); the H2O geometry in the TS of reaction (1) was predicted to significantly deviate from the equilibrium one, whereas the CO2 and H2 geometries in the TS of reaction (2) were found to be more similar to their equilibrium ones. It was also found that the product diatomic molecules, CO and H2, are both vibrationally and rotationally excited. The calculated relative population of the vibrationally excited CO for the 248 nm photodissociation was consistent with experiment.

Atomic topology and optical properties of amorphous porous silicon, ap-Si

Porous silicon has been studied extensively due to the interesting luminous properties that it displays. However, amorphous porous silicon, ap-Si, is an elusive material difficult to produce and study. Since ap-Si can be visualized as highly defective a-Si we have applied our new thermal process, based on an ab initio molecular dynamics method that uses the Harris functional, to generate samples of ap-Si with 50% porosity starting with a cubic periodic supercell of 216 atoms, from which a porous cell was carved out. The randomizing process was done using a 7.5 fs time step and after the various structures were obtained, their optical gaps were determined. We find that the gaps increase monotonically with the randomness of the structure from 0.004 to 0.580 eV.

Amorphous alloys of C 0.5Si 0.5, Si 0.5Ge 0.5 and In 0.5Se 0.5: atomic topology

Using a recently developed ab initio molecular dynamics method based on the Harris functional to amorphize structures of semiconducting elements starting from 64 atom, periodic, diamond-like supercells, we have generated the amorphous structures corresponding to the C 0.5Si 0.5, Si 0.5Ge 0.5 and In 0.5Se 0.5 alloys. We report the atomic topology of the three samples and show that for the C 0.5Si 0.5 a few homonuclear bonds are observed; for Si 0.5Ge 0.5 a large number of homonuclear bonds appear, whereas for In 0.5Se 0.5 each Se is bonded to three In and each In is tetrahedrally bonded to at least three Se.

Microscopic dynamics in the liquid Li-Na alloy: an ab initio molecular dynamics study.

We present results for several structural and dynamical properties of the liquid Li(1-x)Na(x) alloy. The study has been carried out by means of the orbital-free ab initio molecular dynamics method, combined with local ionic pseudopotentials constructed within the same framework. We obtain good agreement with the available experimental data, reproducing accurately, the strong homocoordinating tendencies exhibited by this alloy. The calculated partial dynamic structure factors exhibit clear side peaks whose frequencies, for q<or=0.25 A(-1), correspond to the hydrodynamic sound dispersion of the binary alloy, whereas for larger q values fast and slow sound modes are identified. The mass ratio in this system, m(Na)/m(Li) approximately 3, is the smallest one so far for which the fast mode is observed.

Field theoretic approach to dynamical orbital localization inab initiomolecular dynamics

Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an $\mathrm{SU}(n)$ non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the ``Wannier gauge.'' An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches.

Excited state proton transfer and internal conversion in o-hydroxybenzaldehyde: new insights from non-adiabatic ab initio molecular dynamics

A recently developed non-adiabatic ab initio molecular dynamics method coupling the S1 excited electronic state to the ground state by a surface hopping technique has been applied to study photoexcited o-hydroxybenzaldehyde. Vertical excitation of the enol tautomer to the π π* state leads to spontaneous proton transfer (PT) and thus formation of the keto tautomer. The PT process has been found to be entirely driven by the breathing mode of the H-chelate ring. In fact, there exists no barrier for PT in the S1 state. Non-radiative decay of the π π* excited keto tautomer through internal conversion (IC) is observed on a picosecond time scale. The probability for a non-adiabatic surface hop from the S1 state back to the ground state is seen to be correlated to the chelate ring breathing mode and to the temporal changes in the methoxy OH bond length. There are indications of an increased IC rate associated with the initial PT event.

On-the-fly localization of electronic orbitals in Car-Parrinello molecular dynamics.

The ab initio molecular-dynamics formalism of Car and Parrinello is extended to preserve the locality of the orbitals. The supplementary term in the Lagrangian does not affect the nuclear dynamics, but ensures "on the fly" localization of the electronic orbitals within a periodic supercell in the Gamma-point approximation. The relationship between the resulting equations of motion and the formation of a gauge-invariant Lagrangian combined with a gauge-fixing procedure is briefly discussed. The equations of motion can be used to generate a very stable and easy to implement numerical integration algorithm. It is demonstrated that this algorithm can be used to compute the trajectory of the maximally localized orbitals, known as Wannier orbitals, in ab initio molecular dynamics with only a modest increase in the overall computer time. In the present paper, the new method is implemented within the generalized gradient approximation to Kohn-Sham density-functional theory employing plane wave basis sets and atomic pseudopotentials. In the course of the presentation, we briefly discuss how the present approach can be combined with localized basis sets to design fast linear scaling ab initio molecular-dynamics methods.

Insights into the Electronic Dynamics in Chemical Reactions

We study with an ab initio molecular dynamics method the bond-breaking and bond-forming processes in chemical reactions. To obtain reactive trajectories, we use a newly developed method based on the optimization of a suitably defined action. The Hellmann−Feynman forces, which are needed to optimize the action, are calculated within density-functional theory. We contrast a concerted [4+2] cycloaddition of cyclopentadiene and ethylene with the nonconcerted [2+2] cycloaddition of two ethylene molecules. We find that the duration of the bond-breaking and bond-forming processes due to the nuclear motion is ∼100 fs. Moreover the electronic delocalization, as well as the HOMO−LUMO energy gap during the two reactions, allows us to distinguish clearly between the concerted and the nonconcerted mechanism.

第一原理分子動力学法を用いた化合物半導体の特性解析(J08-2 界面・化合物,J08 原子系の計算力学シミュレーション)

Compound semiconductors have been attracting great research interest over years because of their prominent properties and applications for novel devices. The silicon carbide is also one of them and is used in various conditions. In this study, a shear calculation is performed for a β-silicon carbide on a {111} slip plane sheared in a <110> direction using an ab initio molecular dynamics method and the ideal shear strength and change in the density of states is calculated. We find the ideal shear strength is approximately 37GPa and the band gap becomes narrow as the shear strain increases. We also perform a calculation of a silicon single crystal and discuss the difference in results.

Ab initio centroid path integral molecular dynamics: application to vibrational dynamics of diatomic molecular systems.

An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

Ab initio molecular dynamics study of polarization effects on ionic hydration in aqueous AlCl3 solution

The solvation shell structure and dynamics of Al3+ and Cl− in an aqueous solution of 0.8 M AlCl3 are studied under ambient conditions by using an ab initio molecular dynamics method. The solvation structures obtained from our ab initio simulations are in good agreement with the experimental ones for both Al3+ and Cl−. A detailed analysis of intramolecular geometry of hydration waters and dipole moments of the ingredients shows that the polarization has substantial effects on the structures and dynamics of both the cation and anion hydration shells. Implications for metal hydrolysis of Al3+ will also be given.

Ab initio Monte Carlo simulations for finite-temperature properties: application to lithium clusters and bulk liquid lithium

Ab initio Monte Carlo simulations have been performed to determine the equilibrium properties of liquid lithium and lithium clusters at different temperatures. First-principles density-functional methods were employed to calculate the potential-energy change for each proposed change of configuration, which was then accepted or rejected according to the Metropolis Monte Carlo scheme. The resulting structural properties are compared to data from experimental measurements and ab initio molecular dynamics simulations. It is shown that accurate structural information can be obtained with ab initio Monte Carlo simulations at computational costs comparable to ab initio molecular dynamics methods. We demonstrate that ab initio Monte Carlo simulations for the properties of fairly large condensed-matter systems at nonzero temperatures are feasible.

Structural transformation of methane hydrate from cage clathrate to filled ice

The structural, dynamical, and electronic properties of methane hydrate under pressure and at room temperature are investigated using the ab initio constant pressure molecular dynamics method. Cage structures in cubic structure I are destroyed at 4.5 GPa. After the breakdown of cage structures water molecules form a channel surrounding a chain of methane molecules prominent in MH-III. In our MH-III there exists a single peak of C-D stretching mode showing blueshift in agreement with experiment. Our study supports the existence of “filled ice” proposed by Loveday et al. [Phys. Rev. Lett. 87, 215501 (2001)].