skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: The Chronus Quantum software package
Abstract The Chronus Quantum (ChronusQ) software package is an open source (under the GNU General Public License v2) software infrastructure which targets the solution of challenging problems that arise in ab initio electronic structure theory. Special emphasis is placed on the consistent treatment of time dependence and spin in the electronic wave function, as well as the inclusion of relativistic effects in said treatments. In addition, ChronusQ provides support for the inclusion of uniform finite magnetic fields as external perturbations through the use of gauge‐including atomic orbitals. ChronusQ is a parallel electronic structure code written in modern C++ which utilizes both message passing implementation and shared memory (OpenMP) parallelism. In addition to the examination of the current state of code base itself, a discussion regarding ongoing developments and developer contributions will also be provided. This article is categorized under:Software > Quantum ChemistryElectronic Structure Theory > Ab Initio Electronic Structure MethodsElectronic Structure Theory > Density Functional Theory  more » « less
Award ID(s):
1856210 1624430 1550456
PAR ID:
10447333
Author(s) / Creator(s):
 ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
WIREs Computational Molecular Science
Volume:
10
Issue:
2
ISSN:
1759-0876
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract The two‐electron reduced density matrix (2RDM) carries enough information to evaluate the electronic energy of a many‐electron system. The variational 2RDM (v2RDM) approach seeks to determine the 2RDM directly, without knowledge of the wave function, by minimizing this energy with respect to variations in the elements of the 2RDM, while also enforcing knownN‐representability conditions. In this tutorial review, we provide an overview of the theoretical underpinnings of the v2RDM approach and theN‐representability constraints that are typically applied to the 2RDM. We also discuss the semidefinite programming (SDP) techniques used in v2RDM computations and provide enough Python code to develop a working v2RDM code that interfaces to thelibSDPlibrary of SDP solvers. This article is categorized under:Electronic Structure Theory > Ab Initio Electronic Structure MethodsSoftware > Quantum Chemistry 
    more » « less
  2. Abstract Reliable simulations of molecules in condensed phase require the combination of an accurate quantum mechanical method for the core region, and a realistic model to describe the interaction with the environment. Additionally, this combination should not significantly increase the computational cost of the calculation compared to the corresponding in vacuo case. In this review, we describe the combination of methods based on coupled cluster (CC) theory with polarizable classical models for the environment. We use the polarizable continuum model (PCM) of solvation to discuss the equations, but we also show how the same theoretical framework can be extended to polarizable force fields. The theory is developed within the perturbation theory energy and singles‐T density (PTES) scheme, where the environmental response is computed with the CC single excitation amplitudes as an approximation for the full one‐particle reduced density. The CC‐PTES combination provides the best compromise between accuracy and computational effort for CC calculations in condensed phase, because it includes the response of the environment to the correlation density at the same computational cost of in vacuo CC. We discuss a number of numerical applications for ground and excited state properties, based on the implementation of CC‐PTES with single and double excitations (CCSD‐PTES), which show the reliability and computational efficiency of the method in reproducing experimental or full‐CC data. This article is characterized under:Electronic Structure Theory > Ab Initio Electronic Structure MethodsElectronic Structure Theory > Combined QM/MM MethodsSoftware > Quantum Chemistry 
    more » « less
  3. Abstract This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with the polarizable continuum model, a particular boundary‐element approach to the problem defined by the Poisson or Poisson–Boltzmann equation, but that moniker belies the diversity of available methods. This work reviews the current state‐of‐the art, with emphasis on theory and methods rather than applications. The basics of continuum electrostatics are described, including the nonequilibrium polarization response upon excitation or ionization of the solute. Nonelectrostatic interactions, which must be included in the model in order to obtain accurate solvation energies, are also described. Numerical techniques for implementing the equations are discussed, including linear‐scaling algorithms that can be used in classical or mixed quantum/classical biomolecular electrostatics calculations. Anisotropic models that can describe interfacial solvation are briefly described. This article is categorized under:Electronic Structure Theory > Ab Initio Electronic Structure MethodsMolecular and Statistical Mechanics > Free Energy Methods 
    more » « less
  4. Abstract In silico materials design is hampered by the computational complexity of Kohn–Sham DFT, which scales cubically with the system size. Owing to the development of new‐generation kinetic energy density functionals (KEDFs), orbital‐free DFT (OFDFT) can now be successfully applied to a large class of semiconductors and such finite systems as quantum dots and metal clusters. In this work, we present DFTpy, an open‐source software implementing OFDFT written entirely in Python 3 and outsourcing the computationally expensive operations to third‐party modules, such as NumPy and SciPy. When fast simulations are in order, DFTpy exploits the fast Fourier transforms from PyFFTW. New‐generation, nonlocal and density‐dependent‐kernel KEDFs are made computationally efficient by employing linear splines and other methods for fast kernel builds. We showcase DFTpy by solving for the electronic structure of a million‐atom system of aluminum metal which was computed on a single CPU. The Python 3 implementation is object‐oriented, opening the door to easy implementation of new features. As an example, we present a time‐dependent OFDFT implementation (hydrodynamic DFT) which we use to compute the spectra of small metal clusters recovering qualitatively the time‐dependent Kohn–Sham DFT result. The Python codebase allows for easy implementation of application programming interfaces. We showcase the combination of DFTpy and ASE for molecular dynamics simulations of liquid metals. DFTpy is released under the MIT license. This article is categorized under:Software > Quantum ChemistryElectronic Structure Theory > Density Functional TheoryData Science > Computer Algorithms and Programming 
    more » « less
  5. Abstract Water/oxide interfaces are ubiquitous on earth and show significant influence on many chemical processes. For example, understanding water and solute adsorption as well as catalytic water splitting can help build better fuel cells and solar cells to overcome our looming energy crisis; the interaction between biomolecules and water/oxide interfaces is one hypothesis to explain the origin of life. However, knowledge in this area is still limited due to the difficulty of studying water/solid interfaces. As a result, research using increasingly sophisticated experimental techniques and computational simulations has been carried out in recent years. Although it is difficult for experimental techniques to provide detailed microscopic structural information, molecular dynamics (MD) simulations have satisfactory performance. In this review, we discuss classical and ab initio MD simulations of water/oxide interfaces. Generally, we are interested in the following questions: How do solid surfaces perturb interfacial water structure? How do interfacial water molecules and adsorbed solutes affect solid surfaces and how do interfacial environments affect solvent and solute behavior? Finally, we discuss progress in the application of neural network potential based MD simulations, which offer a promising future because this approach has already enabled ab initio level accuracy for very large systems and long trajectories. This article is categorized under:Theoretical and Physical Chemistry > SpectroscopyMolecular and Statistical Mechanics > Molecular InteractionsStructure and Mechanism > Molecular Structures 
    more » « less