CL2. Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementation, Rapid Development, and Education

A cornerstone of the development of novel quantum chemistry methods is the translation of paper-and-pencil theory into an efficient computer program. To do this, low-level programming languages are typically employed; however, such implementations tend to be convoluted, as raw speed is the focus rather than either readability or reproducibil-ity. Any attempt at re-implementation must then proceed with the originally published equations as the only reference, whereby critical programming details must be re-discovered through a similarly heroic effort to the original implementation. To address these issues, the Psi4NumPy project [1] leverages the Psi4 quantum chemistry package and the Nu-merical Python (NumPy)library to create an interactive quantum chemistry programming environment for reference implementations, rapid development, and education. This envi-ronment allows for quantum chemistry-specific quantities computed with Psi4 and strided tensor manipulations performed with NumPy to be called directly from within the high-level Python programming language. Therefore, implementations of novel methods may be devel-oped quickly and programmed concisely, while maintaining a relatively low execution time. Provided as a series of short Python scripts, reference implementations for a variety of pop-ular quantum chemistry methods (including Hartree–Fock, Møller–Plesset, coupled cluster, electron propagator, and symmetry-adapted perturbation theories) address the community need for clear, readable programs which disseminate the details of such methods’ implemen-tation. Additionally, interactive tutorials discussing both the theory and implementation of these methods and others offer a unique educational framework for novice and experienced quantum chemists alike. Daniel G. A. Smith, Georgia Institute of Technology Dominic A. Sirianni, Georgia Institute of Technology Lori A. Burns, Georgia Institute of Technology Konrad Patkowski, Auburn University C. David Sherrill, Georgia Institute of Technolog

Electronic structure methods for studying non-covalent interactions in complex chemical environments

Non-covalent interactions (NCI) encompass the quantum mechanical forces felt between atoms and molecules which are not directly bonded to one another. Responsible for governing diverse chemical and physical phenomena, NCI are of fundamental interest in fields including materials design and drug discovery, among others. In order to study NCI accurately, quantum chemical methods must be employed whose computational expense often limits the systems which can be studied to at most 100 atoms. Often, this is challenge is addressed by examining NCI in small, representative subsystems, however this approach neglects the influence of chemical environment on these interactions. Furthermore, the best manner in which to study such environmental effects is still an open question in the field. Meeting these challenges will be the focus of this dissertation: through the development of novel quantum chemical methods, as well as the extension of existing methods, this work will seek to describe the effect of diverse chemical environments on non-covalent interactions. In this way, a more complete understanding of these phenomena will be provided, which can then be exploited to advance various chemical applications.Ph.D

Comparison of Explicitly Correlated Methods for Computing High-Accuracy Benchmark Energies for Noncovalent Interactions

The reliability of explicitly correlated methods for providing benchmark-quality noncovalent interaction energies was tested at various levels of theory and compared to estimates of the complete basis set (CBS) limit. For all systems of the A24 test set, computations were performed using both aug-cc-pVXZ (aXZ; X = D, T, Q, 5) basis sets and specialized cc-pVXZ-F12 (XZ-F12; X = D, T, Q, 5) basis sets paired with explicitly correlated coupled cluster singles and doubles [CCSD-F12n (n = a, b, c)] with triple excitations treated by the canonical perturbative method and scaled to compensate for their lack of explicit correlation [(T**)]. Results show that aXZ basis sets produce smaller errors versus the CBS limit than XZ-F12 basis sets. The F12b ansatz results in the lowest average errors for aTZ and larger basis sets, while F12a is best for double-ζ basis sets. When using aXZ basis sets (X ≥ 3), convergence is achieved from above for F12b and F12c ansatzë and from below for F12a. The CCSD­(T**)-F12b/aXZ approach converges quicker with respect to basis than any other combination, although the performance of CCSD­(T**)-F12c/aXZ is very similar. Both CCSD­(T**)-F12b/aTZ and focal point schemes employing density-fitted, frozen natural orbital [DF-FNO] CCSD­(T)/aTZ exhibit similar accuracy and computational cost, and both are much more computationally efficient than large-basis conventional CCSD­(T) computations of similar accuracy

The influence of a solvent environment on direct non-covalent interactions between two molecules: A symmetry-adapted perturbation theory study of polarization tuning of π-π interactions by water

High-level quantum chemical computations have provided significant insight into the fundamental physical nature of non-covalent interactions. These studies have focused primarily on gas-phase computations of small van der Waals dimers; however, these interactions frequently take place in complex chemical environments, such as proteins, solutions, or solids. To better understand how the chemical environment affects non-covalent interactions, we have undertaken a quantum chemical study of π-π interactions in an aqueous solution, as exemplified by T-shaped benzene dimers surrounded by 28 or 50 explicit water molecules. We report interaction energies (IEs) using second-order Møller-Plesset perturbation theory, and we apply the intramolecular and functional-group partitioning extensions of symmetry-adapted perturbation theory (ISAPT and F-SAPT, respectively) to analyze how the solvent molecules tune the π-π interactions of the solute. For complexes containing neutral monomers, even 50 explicit waters (constituting a first and partial second solvation shell) change total SAPT IEs between the two solute molecules by only tenths of a kcal mol-1, while significant changes of up to 3 kcal mol-1 of the electrostatic component are seen for the cationic pyridinium-benzene dimer. This difference between charged and neutral solutes is attributed to large non-additive three-body interactions within solvated ion-containing complexes. Overall, except for charged solutes, our quantum computations indicate that nearby solvent molecules cause very little tuning of the direct solute-solute interactions. This indicates that differences in binding energies between the gas phase and solution phase are primarily indirect effects of the competition between solute-solute and solute-solvent interactions

Physical Chemistry Research at Undergraduate Institutions: Innovative and Impactful Approaches

A tenure-track position at a primarily undergraduate university (PUI) is highly rewarding, but can also be stressful with many new obligations and responsibilities that faculty were not necessarily prepared for during their graduate studies or postdoctoral fellowships. In particular, PUI computational chemists are likely to be the only computational experts in their department, and thus may not have access to experienced mentors to offer advice on establishing and maintaining a successful research group specializing in computational chemistry. In this chapter, we offer faculty beginning a tenure-track position advice and guidance on how to setup a young research lab. We describe several important considerations that faculty must contemplate as they start their labs. Furthermore, we detail different likely scenarios that faculty might encounter based on varying levels of financial, technical, and administrative support at a PUI and how faculty should proceed with establishing a new lab based on their specific situation. Finally, we provide advice for new faculty on how to recruit and train new students, as well as other important decisions faculty must make when trying to build a productive research group. This chapter provides a clear list of the most important aspects of creating a new computational chemistry research group to help new tenure-track faculty get started and be successful in the short- and long-term

Legislative Documents

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P si 4N um P y: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program

psi4/psi4numpy: v0.3-beta

Psi4NumPy is an interactive quantum chemistry framework for development and education. By leveraging the Psi4 program, integrals and quantities important to quantum chemistry are obtained and then manipulated or contracted using the Numerical Python (NumPy) package. In this way, quantum chemistry can be programmed quickly and concisely while still maintaining a relatively low execution time. A series of short scripts are provided that demonstrate how a user would implement the following methods: Self-Consistent Field (SCF), SCF Response, Moller-Plesset Theory, Coupled-Cluster, Symmetry-Adapted Perturbation Theory, and more. Walkthroughs of quantum chemistry methods detailing both their theory and implementation are shown in order to provide an educational framework for both novice and expert users in the field. Overall, this project aims to remove the gap between theory and implementation. As such, user-submitted scripts and modifications are welcome in order to make a better Psi4NumPy experience for the entire quantum chemistry community. As a note, Psi4NumPy is a constantly evolving framework. Please seek github.com/psi4/psi4numpy for the latest version of the code

PSI4 1.4 : Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.Peer reviewe

Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development

Psi4NumPy demonstrates the use of efficient computational kernels from the open- source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Further, several reference codes have been integrated into Jupyter notebooks, allowing background and explanatory information to be associated with the imple- mentation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementa- tions also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program. </div