Michael Aivazis

Python for Scientists and Engineers

Python has arguably become the de facto standard for exploratory, interactive, and computation-driven scientific research. This issue discusses Pythons advantages for scientific research and presents several of the core Python libraries and tools used in scientific research.

GeoFramework: Coupling multiple models of mantle convection within a computational framework

Solver coupling can extend the capability of existing modeling software and provide a new venue to address previously intractable problems. A software package has been developed to couple geophysical solvers, demonstrating a method to accurately and efficiently solve multiscale geophysical problems with reengineered software using a computational framework (Pyre). Pyre is a modeling framework capable of handling all aspects of the specification and launching of numerical investigations. We restructured and ported CitcomS, a finite element code for mantle convection, into the Pyre framework. Two CitcomS solvers are coupled to investigate the interaction of a plume at high resolution with global mantle flow at low resolution. A comparison of the coupled models with parameterized models demonstrates the accuracy and efficiency of the coupled models and illustrates the limitations and utility of parameterized models.

A Virtual Test Facility for the Simulation of Dynamic Response in Materials

The Center for Simulating Dynamic Response of Materials at the California Institute of Technology is constructing a virtual shock physics facility for studying the response of various target materials to very strong shocks. The Virtual Test Facility (VTF) is an end-to-end, fully three-dimensional simulation of the detonation of high explosives (HE), shock wave propagation, solid material response to pressure loading, and compressible turbulence. The VTF largely consists of a parallel fluid solver and a parallel solid mechanics package that are coupled together by the exchange of boundary data. The Eulerian fluid code and Lagrangian solid mechanics model interact via a novel approach based on level sets. The two main computational packages are integrated through the use of Pyre, a problem solving environment written in the Python scripting language. Pyre allows application developers to interchange various computational models and solver packages without recompiling code, and it provides standardized access to several data visualization engines and data input mechanisms. In this paper, we outline the main components of the VTF, discuss their integration via Pyre, and describe some recent accomplishments in large-scale simulation using the VTF.

MCViNE – An object oriented Monte Carlo neutron ray tracing simulation package

MCViNE (Monte-Carlo VIrtual Neutron Experiment) is an open-source Monte Carlo (MC) neutron ray-tracing software for performing computer modeling and simulations that mirror real neutron scattering experiments. We exploited the close similarity between how instrument components are designed and operated and how such components can be modeled in software. For example we used object oriented programming concepts for representing neutron scatterers and detector systems, and recursive algorithms for implementing multiple scattering. Combining these features together in MCViNE allows one to handle sophisticated neutron scattering problems in modern instruments, including, for example, neutron detection by complex detector systems, and single and multiple scattering events in a variety of samples and sample environments. In addition, MCViNE can use simulation components from linear-chain-based MC ray tracing packages which facilitates porting instrument models from those codes. Furthermore it allows for components written solely in Python, which expedites prototyping of new components. These developments have enabled detailed simulations of neutron scattering experiments, with non-trivial samples, for time-of-flight inelastic instruments at the Spallation Neutron Source. Examples of such simulations for powder and single-crystal samples with various scattering kernels, including kernels for phonon and magnon scattering, are presented. With simulations that closely reproduce experimental results, scattering mechanisms can be turned on and off to determine how they contribute to the measured scattering intensities, improving our understanding of the underlying physics.

Development, verification, and maintenance ofcomputational software in geodynamics

Research on dynamical processes within the Earth and planets increasingly relies upon sophisticated, large-scale computational models. Improved understanding of fundamental physical processes such as mantle convection and the geodynamo, magma dynamics, crustal and lithospheric deformation, earthquake nucleation, and seismic wave propagation, are heavily dependent upon better numerical modeling. Surprisingly, the rate-limiting factor for progress in these areas is not just computing hardware, as was once the case. Rather, advances in software are not keeping pace with the recent improvements in hardware. Modeling tools in geophysics are usually developed and maintained by individual scientists, or by small groups. But it is difficult for any individual, or even a small group, to keep up with sweeping advances in computing hardware, parallel processing software, and numerical modeling methodology.