cclib 2.0: An updated architecture for interoperable computational chemistry.

Interoperability in computational chemistry is elusive, impeded by the independent development of software packages and idiosyncratic nature of their output files. The cclib library was introduced in 2006 as an attempt to improve this situation by providing a consistent interface to the results of various quantum chemistry programs. The shared API across programs enabled by cclib has allowed users to focus on results as opposed to output and to combine data from multiple programs or develop generic downstream tools. Initial development, however, did not anticipate the rapid progress of computational capabilities, novel methods, and new programs; nor did it foresee the growing need for customizability. Here, we recount this history and present cclib 2, focused on extensibility and modularity. We also introduce recent design pivots-the formalization of cclib's intermediate data representation as a tree-based structure, a new combinator-based parser organization, and parsed chemical properties as extensible objects.

Periodic Density Matrix Embedding for CO Adsorption on the MgO(001) Surface.

The adsorption of simple gas molecules to metal oxide surfaces is a primary step in many heterogeneous catalysis applications. Quantum chemical modeling of these reactions is a challenge in terms of both cost and accuracy, and quantum-embedding methods are promising, especially for localized chemical phenomena. In this work, we employ density matrix embedding theory (DMET) for periodic systems to calculate the adsorption energy of CO to the MgO(001) surface. Using coupled-cluster theory with single and double excitations and second-order Møller-Plesset perturbation theory as quantum chemical solvers, we perform calculations with embedding clusters up to 266 electrons in 306 orbitals, with the largest embedding models agreeing to within 1.2 kcal/mol of the non-embedding references. Moreover, we present a memory-efficient procedure of storing and manipulating electron repulsion integrals in the embedding space within the framework of periodic DMET.

Exploring Avenues beyond Revised DSD Functionals: I. Range Separation, with xDSD as a Special Case.

We have explored the use of range separation as a possible avenue for further improvement on our revDSD minimally empirical double hybrid functionals. Such ωDSD functionals encompass the XYG3 type of double hybrid (i.e., xDSD) as a special case for ω → 0. As in our previous studies, the large and chemically diverse GMTKN55 benchmark suite was used for evaluation. Especially when using the D4 rather than D3BJ dispersion model, xDSD has a slight performance advantage in WTMAD2. As in previous studies, PBEP86 is the winning combination for the semilocal parts. xDSDn-PBEP86-D4 marginally outperforms the previous "best in class" ωB97M(2) Berkeley double hybrid but without range separation and using fewer than half the number of empirical parameters. Range separation turns out to offer only marginal further improvements on GMTKN55 itself. While ωB97M(2) still yields better performance for small-molecule thermochemistry, this is compensated in WTMAD2 by the superior performance of the new functionals for conformer equilibria. Results for two external test sets with pronounced static correlation effects may indicate that range-separated double hybrids are more resilient to such effects.

The Atomic Partial Charges Arboretum: Trying to See the Forest for the Trees.

Atomic partial charges are among the most commonly used interpretive tools in quantum chemistry. Dozens of different 'population analyses' are in use, which are best seen as proxies (indirect gauges) rather than measurements of a 'general ionicity'. For the GMTKN55 benchmark of nearly 2,500 main-group molecules, which span a broad swathe of chemical space, some two dozen different charge distributions were evaluated at the PBE0 level near the 1-particle basis set limit. The correlation matrix between the different charge distributions exhibits a block structure; blocking is, broadly speaking, by charge distribution class. A principal component analysis on the entire dataset suggests that nearly all variation can be accounted for by just two 'principal components of ionicity': one has all the distributions going in sync, while the second corresponds mainly to Bader QTAIM vs. all others. A weaker third component corresponds to electrostatic charge models in opposition to the orbital-based ones. The single charge distributions that have the greatest statistical similarity to the first principal component are iterated Hirshfeld (Hirshfeld-I) and a minimal-basis projected modification of Bickelhaupt charges. If three individual variables, rather than three principal components, are to be identified that contain most of the information in the whole dataset, one representative for each of the three classes of Corminboeuf et al. is needed: one based on partitioning of the density (such as QTAIM), a second based on orbital partitioning (such as NPA), and a third based on the molecular electrostatic potential (such as HLY or CHELPG).

Ab Initio Finite Temperature Auxiliary Field Quantum Monte Carlo.

We present an ab initio auxiliary field quantum Monte Carlo method for studying the electronic structure of molecules, solids, and model Hamiltonians at finite temperature. The algorithm marries the ab initio phaseless auxiliary field quantum Monte Carlo algorithm known to produce high accuracy ground state energies of molecules and solids with its finite temperature variant, long used by condensed matter physicists for studying model Hamiltonian phase diagrams, to yield a phaseless, ab initio finite temperature method. We demonstrate that the method produces internal energies within chemical accuracy of exact diagonalization results across a wide range of temperatures for H2O (STO-3G), C2 (STO-6G), the one-dimensional hydrogen chain (STO-6G), and the multiorbital Hubbard model. Our method effectively controls the phase problem through importance sampling, often even without invoking the phaseless approximation, down to temperatures at which the systems studied approach their ground states and may therefore be viewed as exact over wide temperature ranges. This technique embodies a versatile tool for studying the finite temperature phase diagrams of a plethora of systems whose properties cannot be captured by a Hubbard U term alone. Our results moreover illustrate that the severity of the phase problem for model Hamiltonians far exceeds that for many molecules at all of the temperatures studied.

CALCULATION OF GAMMA SPECTRA IN A PLASTIC SCINTILLATOR FOR ENERGY CALIBRATIONAND DOSE COMPUTATION.

Plastic scintillation detectors have practical advantages in the field of dosimetry. Energy calibration of measured gamma spectra is important for dose computation, but it is not simple in the plastic scintillators because of their different characteristics and a finite resolution. In this study, the gamma spectra in a polystyrene scintillator were calculated for the energy calibration and dose computation. Based on the relationship between the energy resolution and estimated energy broadening effect in the calculated spectra, the gamma spectra were simply calculated without many iterations. The calculated spectra were in agreement with the calculation by an existing method and measurements.