CRYSTALpytools: A Python infrastructure for the Crystal code

CRYSTALpytools is an open source Python project available on GitHub that implements a user-friendly interface to the Crystal code for quantum-mechanical condensed matter simulations. CRYSTALpytools provides functionalities to: i) write and read Crystal input and output files for a range of calculations (single-point, electronic structure, geometry optimization, harmonic and quasi-harmonic lattice dynamics, elastic tensor evaluation, topological analysis of the electron density, electron transport, and others); ii) extract relevant information; iii) create workflows; iv) post-process computed quantities, and v) plot results in a variety of styles for rapid and precise visual analysis. Furthermore, CRYSTALpytools allows the user to translate Crystal objects (the central data structure of the project) to and from the Structure and Atoms objects of the pymatgen and ASE libraries, respectively. These tools can be used to create, manipulate and visualise complicated structures and write them efficiently to Crystal input files. Jupyter Notebooks have also been developed for the less Python savvy users to guide them in the use of CRYSTALpytools through a user-friendly graphical interface with predefined workflows to complete different specific tasks

Falling into the Echo Chamber: the Italian Vaccination Debate on Twitter

The reappearance of measles in the US and Europe, a disease considered eliminated in early 2000s, has been accompanied by a growing debate on the merits of vaccination on social media. In this study we examine the extent to which the vaccination debate on Twitter is conductive to potential outreach to the vaccination hesitant. We focus on Italy, one of the countries most affected by the latest measles outbreaks. We discover that the vaccination skeptics, as well as the advocates, reside in their own distinct "echo chambers". The structure of these communities differs as well, with skeptics arranged in a tightly connected cluster, and advocates organizing themselves around few authoritative hubs. At the center of these echo chambers we find the ardent supporters, for which we build highly accurate network- and content-based classifiers (attaining 95% cross-validated accuracy). Insights of this study provide several avenues for potential future interventions, including network-guided targeting, accounting for the political context, and monitoring of alternative sources of information

Topology of the Electron Density and of Its Laplacian from Periodic LCAO Calculations on f-Electron Materials: The Case of Cesium Uranyl Chloride

The chemistry of f-electrons in lanthanide and actinide materials is yet to be fully rationalized. Quantum-mechanical simulations can provide useful complementary insight to that obtained from experiments. The quantum theory of atoms in molecules and crystals (QTAIMAC), through thorough topological analysis of the electron density (often complemented by that of its Laplacian) constitutes a general and robust theoretical framework to analyze chemical bonding features from a computed wave function. Here, we present the extension of the Topond module (previously limited to work in terms of s-, p- and d-type basis functions only) of the Crystal program to f- and g-type basis functions within the linear combination of atomic orbitals (LCAO) approach. This allows for an effective QTAIMAC analysis of chemical bonding of lanthanide and actinide materials. The new implemented algorithms are applied to the analysis of the spatial distribution of the electron density and its Laplacian of the cesium uranyl chloride, Cs2UO2Cl4, crystal. Discrepancies between the present theoretical description of chemical bonding and that obtained from a previously reconstructed electron density by experimental X-ray diffraction are illustrated and discussed

Thermo-Elasticity of Materials from Quasi-Harmonic Calculations

An effective algorithm for the quasi-harmonic calculation of thermo-elastic stiffness constants of materials is discussed and implemented into the Crystal program for quantum-mechanical simulations of extended systems. Two different approaches of increasing complexity and accuracy are presented. The first one is a quasi-static approximation where the thermal dependence of elastic constants is assumed to be due only to the thermal expansion of the system. The second one is fully quasi-harmonic, takes into account thermal expansion, and explicitly computes Helmholtz free energy derivatives with respect to strain. The conversion of isothermal into adiabatic thermo-elastic constants is also addressed. The algorithm is formally presented and applied to the description of the thermo-elastic response of the forsterite mineral