Stacking of oligo and polythiophenes cations in solution: surface tension and dielectric saturation

The stacking of positively charged (or doped) terthiophene oligomers and quaterthiophene polymers in solution is investigated applying a recently developed unified electrostatic and cavitation model for first-principles calculations in a continuum solvent. The thermodynamic and structural patterns of the dimerization are explored in different solvents, and the distinctive roles of polarity and surface tension are characterized and analyzed. Interestingly, we discover a saturation in the stabilization effect of the dielectric screening that takes place at rather small values of $\epsilon_0$. Moreover, we address the interactions in trimers of terthiophene cations, with the aim of generalizing the results obtained for the dimers to the case of higher-order stacks and nanoaggregates

A fast, dense Chebyshev solver for electronic structure on GPUs

Matrix diagonalization is almost always involved in computing the density matrix needed in quantum chemistry calculations. In the case of modest matrix sizes ($\lesssim$ 5000), performance of traditional dense diagonalization algorithms on modern GPUs is underwhelming compared to the peak performance of these devices. This motivates the exploration of alternative algorithms better suited to these types of architectures. We newly derive, and present in detail, an existing Chebyshev expansion algorithm [W. Liang et al, J. Chem. Phys. 2003] whose number of required matrix multiplications scales with the square root of the number of terms in the expansion. Focusing on dense matrices of modest size, our implementation on GPUs results in large speed ups when compared to diagonalization. Additionally, we improve upon this existing method by capitalizing on the inherent task parallelism and concurrency in the algorithm. This improvement is implemented on GPUs by using CUDA and HIP streams via the MAGMA library and leads to a significant speed up over the serial-only approach for smaller ($\lesssim$ 1000) matrix sizes. Lastly, we apply our technique to a model system with a high density of states around the Fermi level which typically presents significant challenges.Comment: Submitted to Journal of Chemical Physics Communication

O(N) real-space method for ab initio quantum transport calculations: Application to carbon nanotube - metal contacts

Article on O(N) real-space method for ab initio quantum transport calculations and application to carbon nanotube-metal contacts

Workshop report. Linear-Scaling Ab Initio Calculations: Applications and Future Directions

The study of properties and of processes in materials, frequently hinges upon understanding phenomena which originate at the atomic level. In such cases the accurate description of the interactions between large numbers of atoms is critical and in turn requires the accurate description of the electrons which play a crucial role in the bonding of atoms into molecules, surfaces and solids. This can only be achieved by solving the equations of quantum mechanics. These equations are too complicated to solve exactly; however their solutions can be approximated by computational techniques. The most accurate ? but also most computationally demanding ? are the “ab initio” techniques which do not use any empirical adjustable parameters. Amongst them, the Density Functional Theory (DFT) formulation of quantum mechanics stands out as an excellent compromise between accuracy and computational efficiency. However, the applicability of ab initio techniques is severely limited by poor scaling: the computational effort needed to perform an ab initio calculation increases with (at least) the third power of the number of atoms, N. This cubic-scaling bottleneck limits the number of atoms we can study to a few hundred at most, even on parallel supercomputers. To overcome this length-scale limitation, a number of researchers worldwide have been pioneering the development of a novel class of ab initio methods with linear-scaling or “Order N” (O(N)) computational cost which nevertheless retain the same high level of accuracy as the conventional approaches. While physically motivated, such methods have proved particularly hard to develop as they introduce highly non-trivial localisation constraints. Nevertheless, many major obstacles have been overcome and a number of O(N) methods (SIESTA, CONQUEST, ONETEP, etc.) for ground state DFT calculations on systems with a gap (e.g. molecules, semiconductors and insulators) are now available and have reached a state of maturity that allows them to be used to study ”real” materials. The particular focus of this workshop is therefore to look forward to what can be achieved in the next few years. Our aim is twofold: (1) As O(N) methods are currently extending the applicability of DFT calculations to problems involving biomolecules and nanostructures they are leading to completely new levels of understanding of these systems. This CECAM meeting will give us the opportunity to make an appraisal of such large-scale simulations and their potential to connect more directly to experiments. (2) We also want to examine the options for extending linear-scaling to problems that cannot be treated by ground-state DFT but require other, more complex approaches. These include methods for treating metallic systems, excited states and wavefunction-based theories for including electronic correlation. Finding ways to transform these methods to linear-scaling cost, and hence extent their applicability to the nano-scale, is the next big challenge that the community of developers of large-scale electronic structure methods is beginning to face. We hope that this workshop will stimulate these major new O(N) methodological developments by bringing together the leading groups in the development of O(N) DFT methods with the leading groups in the development of metal and excited-state or wavefunction-based methods. Strong emphasis during the workshop will be given to discussion in order to promote the exchange of ideas between different communities (Physics, Chemistry, Materials Science, Biochemistry) which are all interested in large-scale applications with ab initio accuracy but are approaching them from different perspectives

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

The electrostatic continuum solvent model developed by Fattebert and Gygi is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution, and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon

A BLOCK RAYLEIGH QUOTIENT ITERATION WITH LOCAL QUADRATIC CONVERGENCE

Abstract. We present an iterative method, based on a block generalization of the Rayleigh Quotient Iteration method, to search for the p lowest eigenpairs of the generalized matrix eigenvalue problem Au = Bu. We prove its local quadratic convergence when B,1 A is symmetric. The benefits of this method are the well-conditioned linear systems produced and the ability to treat multiple or nearly degenerate eigenvalues. Key words. Subspace iteration, Rayleigh Quotient Iteration, Rayleigh-Ritz procedure. AMS subject classifications. 65F15

Linear scaling first-principles molecular dynamics with controlled accuracy

We propose a real-space finite differences approach for accurate and unbiased O(N) Density Functional Theory molecular dynamics simulations based on a localized orbitals representation of the electronic structure. The discretization error can be reduced systematically by adapting the mesh spacing, while the orbitals truncation error decreases exponentially with the radius of the localization regions. For regions large enough, energy conservation in microcanonical simulations is demonstrated for liquid water. We propose an explanation for the energy drift observed for smaller regions