Developing a Computational Chemistry Framework for the Exascale Era

Within computational chemistry, the NWChem package has arguably been the de facto standard for running high-accuracy numerical simulations on the most powerful supercomputers. In order to better address the challenges presented by emerging exascale architectures, the decision has been made to rewrite NWChem. Design of the resulting package, NWChemEx, has been driven by exascale computing; however, significant additional design considerations have arisen from the team\u27s involvement with the Molecular Sciences Software Institute (MolSSI). MolSSI is a National Science Foundation initiative focused on establishing coding and data standards for the computational chemistry community. As a result, NWChemEx is built upon a general computational chemistry framework called the simulation development environment (SDE) that is designed with a focus on extensibility and interoperability. The present manuscript describes the modular approach of the SDE and how it has been used to implement the self-consistent field algorithm within NWChemEx

Recent Developments in the General Atomic and Molecular Electronic Structure System

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized

Using quantum chemistry muscle to flex massive systems: How to respond to something perturbing

In general, it is difficult to balance accuracy and computational cost in quantum chemistry calculations. One method of approaching this problem is by using classical force field methods, and another is by simplifying ab initio methods. This document discusses a merging of the two approaches, and specifically the Effective Fragment Molecular Orbital method. The fully analytic gradient for the Effective Fragment Molecular Orbital method is derived, and the implementation and accuracy are discussed. Different sets of multipole moments in the general Effective Fragment Potential method are benchmarked. Calculating the melting temperature of water using the Effective Fragment Molecular Orbital method is discussed.</p

VALENCE-software/VALENCE: Open source release of VALENCE

First release of VALENCE quantum chemistry softwar

Analytic Gradients for the Effective Fragment Molecular Orbital Method

The analytic gradient for the Coulomb, polarization, exchange-repulsion, and dispersion terms of the fully integrated effective fragment molecular orbital (EFMO) method is derived and the implementation is discussed. The derivation of the EFMO analytic gradient is more complicated than that for the effective fragment potential (EFP) gradient, because the geometry of each EFP fragment is flexible (not rigid) in the EFMO approach. The accuracy of the gradient is demonstrated by comparing the EFMO analytic gradient with the numeric gradient for several systems, and by assessing the energy conservation during an EFMO NVE ensemble molecular dynamics simulation of water molecules. In addition to facilitating accurate EFMO geometry optimizations, this allows calculations with flexible EFP fragments to be performed

Valence: A Massively Parallel Implementation of the Variational Subspace Valence Bond Method

This work describes the software package, Valence, for the calculation of molecularenergies using the variational subspace valence bond (VSVB) method. VSVB is a highly scalable ab initio electronic structure method based on non-orthogonal orbitals. Important features of practical value include: Valence bond wave functions of Hartree–Fock quality can be constructed with a single determinant; excited states can be modeled with a single configuration or determinant; wave functions can be constructed automatically by combining orbitals from previous calculations. The opensource software package includes tools to generate wave functions, a database of generic orbitals, example input files, and a library build intended for integration with other packages. We also describe the interface to an external software package, enabling the computation of optimized molecular geometries and vibrational frequencies

Efficient and Accurate Fragmentation Methods

Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum mechanical calculations on fragment–fragment (dimer) interactions. The EFMO method is both more accurate and more computationally efficient than the most commonly used FMO implementation (FMO2), in which all dimers are explicitly included in the calculation. While the FMO2 method itself does not incorporate three-body interactions, such interactions are included in the EFMO method via the EFP self-consistent induction term. Several applications (ranging from clusters to proteins) of the three methods are discussed to demonstrate their efficacy. The EFMO method will be especially exciting once the analytic gradients have been completed, because this will allow geometry optimizations, the prediction of vibrational spectra, reaction path following, and molecular dynamics simulations using the method.Reprinted (adapted) with permission from Accounts of Chemical Research 47 (2014): 2786, doi:10.1021/ar500097m. Copyright 2014 American Chemical Society.</p

Multipole Moments in the Effective Fragment Potential Method

In the effective fragment potential (EFP) method the Coulomb potential is represented using a set of multipole moments generated by the distributed multipole analysis (DMA) method. Misquitta, Stone, and Fazeli recently developed a basis space-iterated stockholder atom (BS-ISA) method to generate multipole moments. This study assesses the accuracy of the EFP interaction energies using sets of multipole moments generated from the BS-ISA method, and from several versions of the DMA method (such as analytic and numeric grid-based), with varying basis sets. Both methods lead to reasonable results, although using certain implementations of the DMA method can result in large errors. With respect to the CCSD(T)/CBS interaction energies, the mean unsigned error (MUE) of the EFP method for the S22 data set using BS-ISA–generated multipole moments and DMA-generated multipole moments (using a small basis set and the analytic DMA procedure) is 0.78 and 0.72 kcal/mol, respectively. The MUE accuracy is on the same order as MP2 and SCS-MP2. The MUEs are lower than in a previous study benchmarking the EFP method without the EFP charge transfer term, demonstrating that the charge transfer term increases the accuracy of the EFP method. Regardless of the multipole moment method used, it is likely that much of the error is due to an insufficient short-range electrostatic term (i.e., charge penetration term), as shown by comparisons with symmetry-adapted perturbation theory.This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in The Journal of Physical Chemistry, copyright © 2017 American Chemical Society after peer review. To access the final edited and published work see DOI: 10.1021/acs.jpca.7b00682. Posted with permission