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Feb 19

Directional Message Passing for Molecular Graphs

Graph neural networks have recently achieved great successes in predicting quantum mechanical properties of molecules. These models represent a molecule as a graph using only the distance between atoms (nodes). They do not, however, consider the spatial direction from one atom to another, despite directional information playing a central role in empirical potentials for molecules, e.g. in angular potentials. To alleviate this limitation we propose directional message passing, in which we embed the messages passed between atoms instead of the atoms themselves. Each message is associated with a direction in coordinate space. These directional message embeddings are rotationally equivariant since the associated directions rotate with the molecule. We propose a message passing scheme analogous to belief propagation, which uses the directional information by transforming messages based on the angle between them. Additionally, we use spherical Bessel functions and spherical harmonics to construct theoretically well-founded, orthogonal representations that achieve better performance than the currently prevalent Gaussian radial basis representations while using fewer than 1/4 of the parameters. We leverage these innovations to construct the directional message passing neural network (DimeNet). DimeNet outperforms previous GNNs on average by 76% on MD17 and by 31% on QM9. Our implementation is available online.

  • 3 authors
·
Mar 6, 2020

High-order finite element method for atomic structure calculations

We introduce featom, an open source code that implements a high-order finite element solver for the radial Schr\"odinger, Dirac, and Kohn-Sham equations. The formulation accommodates various mesh types, such as uniform or exponential, and the convergence can be systematically controlled by increasing the number and/or polynomial order of the finite element basis functions. The Dirac equation is solved using a squared Hamiltonian approach to eliminate spurious states. To address the slow convergence of the kappa=pm1 states due to divergent derivatives at the origin, we incorporate known asymptotic forms into the solutions. We achieve a high level of accuracy (10^{-8} Hartree) for total energies and eigenvalues of heavy atoms such as uranium in both Schr\"odinger and Dirac Kohn-Sham solutions. We provide detailed convergence studies and computational parameters required to attain commonly required accuracies. Finally, we compare our results with known analytic results as well as the results of other methods. In particular, we calculate benchmark results for atomic numbers (Z) from 1 to 92, verifying current benchmarks. We demonstrate significant speedup compared to the state-of-the-art shooting solver dftatom. An efficient, modular Fortran 2008 implementation, is provided under an open source, permissive license, including examples and tests, wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines.

  • 8 authors
·
Jul 11, 2023

Drift surface solver for runaway electron current dominant equilibria during the Current Quench

Runaway electron current generated during the Current Quench phase of tokamak disruptions could result in severe damage to future high performance devices. To control and mitigate such runaway electron current, it is important to accurately describe the runaway electron current dominated equilibrium, based on which further stability analysis could be carried out. In this paper, we derive a Grad-Shafranov-like equation solving for the axisymmetric drift surfaces of the runaway electrons for the simple case that all runaway electron share the same parallel momentum. This new equilibrium equation is then numerically solved with simple rectangular wall with ITER-like and MAST-like geometry parameters. The deviation between the drift surfaces and the flux surfaces is readily obtained, and runaway electrons is found to be well confined even in regions with open field lines. The change of the runaway electron parallel momentum is found to result in a horizontal current center displacement without any changes in the total current or the external field. The runaway current density profile is found to affect the susceptibility of such displacement, with flatter profiles result in more displacement by the same momentum change. With up-down asymmetry in the external poloidal field, such displacement is accompanied by a vertical displacement of runaway electron current. It is found that this effect is more pronounced in smaller, compact device and weaker poloidal field cases. The above results demonstrate the dynamics of current center displacement caused by the momentum space change in the runaway electrons, and pave way for future, more sophisticated runaway current equilibrium theory with more realistic consideration on the runaway electron momentum distribution. This new equilibrium theory also provides foundation for future stability analysis of the runaway electron current.

  • 2 authors
·
Mar 2, 2023