Erik Deumens

Parallel implementation of electronic structure energy, gradient, and Hessian calculations

ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree-Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensive operations, such as tensor contractions and diagonalizations, all communication operations, and all input-output operations are handled by a parallel program written in C and FORTRAN 77. This parallel program, called the super instruction processor (SIP), interprets and executes the SIAL program. By separating the algorithmic complexity (in SIAL) from the complexities of execution on computer hardware (in SIP), a software system is created that allows for very effective optimization and tuning on different hardware architectures with quite manageable effort.

Time‐dependent dynamics of electrons and nuclei

Using the time‐dependent variational principle with a group theoretical coherent state defining the wave functions for electrons and nuclei, a system of coupled, first‐order, nonlinear differential equations is obtained for a general molecular system. The equations form a classical Hamiltonian system within a generalized phase space that allows a systematic time‐dependent study of molecular processes. The approach is general and provides a computational framework for a variety of properties such as transition and excitation probabilities in atomic and molecular collisions, and molecular spectra such as vibrational spectra with anharmonicities. The basic approximation corresponding to the choice of a single determinantal wave function for the electrons and classical nuclei is analyzed. Illustrative applications to the p+H collision process and to vibrations of the H2O molecule exhibit good agreement with experiment and with other theoretical work.

Vibrations and soliton dynamics of positively charged polyacetylene chains

Ab initio molecular dynamics simulation is performed on a small polyacetylene chain with a positive soliton defect. The dynamics is initialized by an external electric field. The collective motion of the carbon and hydrogen atoms are compared to some low frequency vibrational modes of positively charged polyacetylene chains of varying lengths having the characteristics of the soliton displacement. The soliton effective mass estimated using a variety of schemes is found to be about 10 electron masses. The static linear polarizability of singly charged polyacetylene chains of varying lengths is computed and compared with that of undoped chains. The electronic contributions to the polarizability are computed at the level of the coupled Hartree–Fock or the random phase approximation, and the vibrational contributions are estimated by invoking the double harmonic oscillator approximation. The soliton defect causes some enhancement of the electronic term, which covers 10–15 carbon–carbon double bonds, and it ge...

Electron nuclear dynamics of H++H2 collisions at Elab=30 eV

Proton collisions with hydrogen molecules at 30 eV in the laboratory frame is a simple ion‐molecule system exhibiting a number of distinct processes such as inelastic scattering, charge transfer, rearrangement, and dissociation. The electron nuclear dynamics (END) theory which allows full electron nuclear coupling and which does not restrict the system from reaching any of the possible product channels, is applied to this sytem to produce transition probabilities, differential, and integral (vibrationally resolved) cross sections. Comparisons with experiment demonstrate that END, even in its simplest implementation, with a single determinantal state for the electrons and with classical nuclei, yields results that are competitive with other theoretical approaches.

The Sp(2, R) model applied to 8Be

Abstract We work out the complete Sp(2, R ) model for the low-lying states of 8 Be. The calculation in the infinite dimensional representation space is performed with the generator coordinate method. The spectrum shows a marked departure from truncated Sp(2, R ) results and compares favourably with experiment.

Electron nuclear dynamics of proton collisions with methane at 30 eV

The reactive collisions of protons with methane molecules at 30 eV in the laboratory frame are studied with the electron nuclear dynamics (END). The results from this theoretical approach, which does not invoke the Born–Oppenheimer approximation and does not impose any constraints on the nuclear dynamics, are compared to the results from time-of-flight measurements. Total differential cross sections and integral cross sections as well as fragmentation ratios and energy loss spectra are discussed.

Coherent state formulation of multiconfiguration states

The theory of vector coherent states is applied to multiconfiguration states that are given a complex parametrization, based on the underlying special linear group. Using the time‐dependent variational principle, equations of motion for such states are formulated as evolution equations in a generalized phase space. The classical Hamiltonian for these equations is given in terms of the reduced first‐ and second‐order density matrices, which can be expressed in terms of partial derivatives with respect to the group parameters of the overlap kernel. The multiconfiguration self‐consistent‐field (MCSCF) and configuration interaction (CI) equations arise as special cases of these equations. Using the coherent state formulation we obtain very compact and numerically efficient expressions for the time‐dependent quantum mechanical description of chemical reactions.

Software design of ACES III with the super instruction architecture

The Advanced Concepts in Electronic Structure (ACES) III software is a completely rewritten implementation for parallel computer architectures of the most used capabilities in ACES II, including the calculation of the electronic structure of molecular ground states and excited states, and determination of molecular geometries and of vibrational frequencies using many‐body and coupled cluster methods. To achieve good performance on modern parallel systems while simultaneously offering a software development environment that allows rapid implementation of new methods and algorithms, ACES III was written using a new software infrastructure, the super instruction architecture comprising a domain‐specific language, super instruction assembly language (SIAL), and a sophisticated runtime environment, super instruction processor (SIP). The architecture of ACES III is described as well as the inner workings of SIAL and SIP. The execution performance of ACES III and the productivity of programming in SIAL are discussed.

A versatile AMBER‐Gaussian QM/MM interface through PUPIL

The PUPIL package (Program for User Package Interfacing and Linking) originally was developed to interface different programs for multiscale calculations in materials sciences (Torras et al., J Comput Aided Mater Des 2006, 13, 201; Torras et al., Comput Phys Commun 2007, 177, 265). Here we present an extension of PUPIL to computational chemistry by interfacing two widely used computational chemistry programs: AMBER (molecular dynamics) and Gaussian (quantum chemistry). The benefit is to allow the application of the advanced MD techniques available in AMBER to a hybrid QM/MM system in which the forces and energy on the QM part can be computed by any of the methods available in Gaussian. To illustrate, we present two example applications: A MD calculation of alanine dipeptide in explicit water, and a use of the steered MD capabilities in AMBER to calculate the free energy of reaction for the dissociation of Angelis salt.

On rotational coherent states in molecular quantum dynamics

Coherent states suitable for the description of molecular rotations are developed and their connection to similar coherent states in the literature are explored. In particular their quasiclassical properties are developed. The use of such coherent states in time-dependent electron nuclear dynamics studies of molecular collision processes is discussed.