Developing interoperable, accessible software via the atomic, molecular, and optical sciences gateway: A case study of the B-spline atomic R-matrix code graphical user interface.

The Atomic, Molecular, and Optical Science (AMOS) Gateway is a comprehensive cyberinfrastructure for research and educational activities in computational AMO science. The B-Spline atomic R-Matrix (BSR) suite of programs is one of several computer programs currently available on the gateway. It is an excellent example of the gateway's potential to increase the scientific productivity of AMOS users. While the suite is available to be used in batch mode, its complexity does not make it well-suited to the approach taken in the gateway's default setup. The complexity originates from the need to execute many different computations and to construct generally complex workflows, requiring numerous input files that must be used in a specific sequence. The BSR graphical user interface described in this paper was developed to considerably simplify employing the BSR codes on the gateway, making BSR available to a large group of researchers and students interested in AMO science.

A few selected contributions to electron and photon collisions with H2 and H 2 + .

We discuss a number of aspects regarding the physics of H 2 + and H2. This includes low-energy electron scattering processes and the interaction of both weak (perturbative) and strong (ultrafast/intense) electromagnetic radiation with those systems.

How Novel Algorithms and Access to High Performance Computing Platforms are Enabling Scientific Progress in Atomic and Molecular Physics.

Over the past 40 years there has been remarkable progress in the quantitative treatment of complex many-body problems in atomic and molecular physics (AMP). This has happened as a consequence of the development of new and powerful numerical methods, translating these algorithms into practical software and the associated evolution of powerful computing platforms ranging from desktops to high performance computational instruments capable of massively parallel computation. We are taking the opportunity afforded by this CCP2015 to review computational progress in scattering theory and the interaction of strong electromagnetic fields with atomic and molecular systems from the early 1960's until the present time to show how these advances have revealed a remarkable array of interesting and in many cases unexpected features. The article is by no means complete and certainly reflects the views and experiences of the author.

DFT-Based Permutationally Invariant Polynomial Potentials Capture the Twists and Turns of C14H30.

Hydrocarbons are ubiquitous as fuels, solvents, lubricants, and as the principal components of plastics and fibers, yet our ability to predict their dynamical properties is limited to force-field mechanics. Here, we report two machine-learned potential energy surfaces (PESs) for the linear 44-atom hydrocarbon C14H30 using an extensive data set of roughly 250,000 density functional theory (DFT) (B3LYP) energies for a large variety of configurations, obtained using MM3 direct-dynamics calculations at 500, 1000, and 2500 K. The surfaces, based on Permutationally Invariant Polynomials (PIPs) and using both a many-body expansion approach and a fragmented-basis approach, produce precise fits for energies and forces and also produce excellent out-of-sample agreement with direct DFT calculations for torsional and dihedral angle potentials. Going beyond precision, the PESs are used in molecular dynamics calculations that demonstrate the robustness of the PESs for a large range of conformations. The many-body PIPs PES, although more compute intensive than the fragmented-basis one, is directly transferable for other linear hydrocarbons.

Graph convolutional neural network applied to the prediction of normal boiling point.

In this article, we describe training and validation of a machine learning model for the prediction of organic compound normal boiling points. Data are drawn from the experimental literature as captured in the NIST Thermodynamics Research Center (TRC) SOURCE Data Archival System. The machine learning model is based on a graph neural network approach, a methodology that has proven powerful when applied to a variety of chemical problems. Model input is extracted from a 2D sketch of the molecule, making the methodology suitable for rapid prediction of normal boiling points in a wide variety of scenarios. Our final model predicts normal boiling points within 6 K (corresponding to a mean absolute percent error of 1.32%) with sample standard deviation less than 8 K. Additionally, we found that our model robustly identifies errors in the input data set during the model training phase, thereby further motivating the utility of systematic data exploration approaches for data-related efforts.

Predicting Kováts Retention Indices Using Graph Neural Networks.

The Kováts retention index is a dimensionless quantity that characterizes the rate at which a compound is processed through a gas chromatography column. This quantity is independent of many experimental variables and, as such, is considered a near-universal descriptor of retention time on a chromatography column. The Kováts retention indices of a large number of molecules have been determined experimentally. The "NIST 20: GC Method/Retention Index Library" database has collected and, more importantly, curated retention indices of a subset of these compounds resulting in a highly valued reference database. The experimental data in the library form an ideal data set for training machine learning models for the prediction of retention indices of unknown compounds. In this article, we describe the training of a graph neural network model to predict the Kováts retention index for compounds in the NIST library and compare this approach with previous work [1]. We predict the Kováts retention index with a mean unsigned error of 28 index units as compared to 44, the putative best result using a convolutional neural network [1]. The NIST library also incorporates an estimation scheme based on a group contribution approach that achieves a mean unsigned error of 114 compared to the experimental data. Our method uses the same input data source as the group contribution approach, making its application straightforward and convenient to apply to existing libraries. Our results convincingly demonstrate the predictive powers of systematic, data-driven approaches leveraging deep learning methodologies applied to chemical data and for the data in the NIST 20 library outperform previous models.

Parallel solver for the time-dependent linear and nonlinear Schrödinger equation.

A solution of the time-dependent Schrödinger equation is required in a variety of problems in physics and chemistry. These include atoms and molecules in time-dependent electromagnetic fields, time-dependent approaches to atomic collision problems, and describing the behavior of materials subjected to internal and external forces. We describe an approach in which the finite-element discrete variable representation (FEDVR) is combined with the real-space product (RSP) algorithm to generate an efficient and highly accurate method for the solution of the time-dependent linear and nonlinear Schrödinger equation. The FEDVR provides a highly accurate spatial representation using a minimum number of grid points while the RSP algorithm propagates the wave function in operations per time step. Parallelization of the method is transparent and is implemented here by distributing one or two spatial dimensions across the available processors, within the message-passing-interface scheme. The complete formalism and a number of three-dimensional examples are given; its high accuracy and efficacy are illustrated by a comparison with the usual finite-difference method.

Discrete variable representation for singular Hamiltonians.

We discuss the application of the discrete variable representation (DVR) to Schrödinger problems which involve singular Hamiltonians. Unlike recent authors who invoke transformations to rid the eigenvalue equation of singularities at the cost of added complexity, we show that an approach based solely on an orthogonal polynomial basis is adequate, provided the Gauss-Lobatto or Gauss-Radau quadrature rule is used. This ensures that the mesh contains the singular points and by simply discarding the DVR functions corresponding to those points, all matrix elements become well behaved, the boundary conditions are satisfied, and the calculation is rapidly convergent. The accuracy of the method is demonstrated by applying it to the hydrogen atom. We emphasize that the method is equally capable of describing bound states and continuum solutions.