Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science.

Anna Krylov,Robert J Harrison,Theresa L Windus,T Daniel Crawford,Shantenu Jha,Doaa Altarawy,Daniel G A Smith,Jessica A Nash,Benjamin Pritchard,Vijay S Pande,Eliseo Marin-Rimoldi,Paul Saxe,Taylor Barnes,Teresa Head-Gordon,Cecilia Clementi

doi:10.1063/1.5052551

Abstract

The field of computational molecular sciences (CMSs) has made innumerable contributions to the understanding of the molecular phenomena that underlie and control chemical processes, which is manifested in a large number of community software projects and codes. The CMS community is now poised to take the next transformative steps of better training in modern software design and engineering methods and tools, increasing interoperability through more systematic adoption of agreed upon standards and accepted best-practices, overcoming unnecessary redundancy in software effort along with greater reproducibility, and increasing the deployment of new software onto hardware platforms from in-house clusters to mid-range computing systems through to modern supercomputers. This in turn will have future impact on the software that will be created to address grand challenge science that we illustrate here: the formulation of diverse catalysts, descriptions of long-range charge and excitation transfer, and development of structural ensembles for intrinsically disordered proteins.

Highlights

These scientific breakthroughs have been made possible by the evolution of dozens of computational molecular sciences (CMSs) community codes— some with lifetimes reaching back to the earliest days of computing—which include both open-source and commercial packages
We show that the theoretical, methodological, and algorithmic advances that provide the scientific approaches to these problems—i.e., what individual research groups excel at and where all of the true innovation will come from— will be the underlying engines for the software projects that Molecular Sciences Software Institute (MolSSI) can address in these grand challenge scientific use cases
The first requirement is a continuum model for the species transport and reaction in a 1-D electrochemical cell; a microkinetic model is needed to describe the rates at which each product is formed to feed up to the continuum model; and Kohn-Sham (KS) Density Functional Theory (DFT)36 is used to characterize intermediates and reaction barriers, which are supplied to the microkinetic model

Summary

INTRODUCTION

These scientific breakthroughs have been made possible by the evolution of dozens of CMS community codes— some with lifetimes reaching back to the earliest days of computing—which include both open-source and commercial packages. There can be specific methodological and software niches served by different packages This leads to the lack of algorithmic interoperability between codes, in which the current standard is to duplicate the most standard algorithms in each software platform, which can be inefficient, prone to translational errors, and suppresses innovation for new methodology. The MolSSI continues to sponsor multiple software workshops for the purpose of understanding the different needs of the diverse CMS community through capturing requirements and active development of use cases. The MolSSI endeavors to fundamentally and dramatically improve molecular science software development to benefit the CMS community As a result, this new software infrastructure and support will create opportunities for new levels of scientific questions to be asked and answered.

CATALYST DESIGN

LONG-RANGE CHARGE AND EXCITATION TRANSFER

INTRINSICALLY DISORDERED PROTEINS

EARLY SOFTWARE EFFORTS AT THE MolSSI

Findings

CONCLUSION