A tool for the interactive 3D visualization of electronic structure in molecules and solids (original) (raw)
Related papers
2008
Abstract This paper presents the VASP data viewer, a desktop 3D visualization application for the analysis of electronic structure information derived from ab-initio quantummechanical density functional calculations. This tool allows a scientist to directly view and manipulate the calculated charge density from an electronic structure calculation, providing insight into the nature of chemical bonding. Particular attention was given to the design and implementation of the user interface for the data viewer.
MoleCoolQt – a molecule viewer for charge-density research
Journal of Applied Crystallography, 2011
MoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for example, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso, color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms -as sometimes required for local atomic coordinate systems -are calculated on demand; XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD, MoPro, SHELX, GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS.
Theoretical Chemistry Accounts, 2007
This paper overviews the work made by our group during the past 10-15 years on crystalline systems, semiconductor surfaces, molecular complexes and on materials of interest for technological applications, such as the defective silicon or the novel generation thermoelectric materials. Our main aim of extracting chemical insight into the analysis of electron densities and computed wave functions is illustrated through a number of examples. The recently proposed Source Function analysis is reviewed and a few of its more interesting applications are summarized. Software package developments, motivated by the need of a direct comparison with experiment or by the help these packages can provide for interpreting complex experimental outcomes, are described and future directions outlined. A particular emphasis is given to the TOPOND and TOPXD programs, which enable one to analyze theoretical and experimental crystalline densities using the rigorous framework of the Quantum Theory of Atoms in Molecules, due to Bader.
Journal of Chemical Theory and Computation, 2011
We present a modified definition of the Electron Pair Localization Function (EPLF), initially defined within the framework of quantum Monte Carlo approaches Chaquin, P. J. Chem. Phys. 2004, 121, 1725 to be used in Density Functional Theories (DFT) and ab initio wave-function-based methods. This modified version of the EPLF-while keeping the same physical and chemical contents-is built to be analytically computable with standard wave functions or Kohn-Sham representations. It is illustrated that the EPLF defines a simple and powerful tool for chemical interpretation via selected applications including atomic and molecular closed-shell systems, σ and π bonds, radical and singlet open-shell systems, and molecules having a strong multiconfigurational character. Some applications of the EPLF are presented at various levels of theory and compared to Becke and Edgecombe's Electron Localization Function (ELF). Our open-source parallel software implementation of the EPLF opens the possibility of its use by a large community of chemists interested in the chemical interpretation of complex electronic structures.
Q-Chem 2.0: a high-performanceab initio electronic structure program package
Journal of Computational Chemistry, 2000
Q-Chem 2.0 is a new release of an electronic structure program package, capable of performing first principles calculations on the ground and excited states of molecules using both density functional theory and wave function-based methods. A review of the technical features contained within Q-Chem 2.0 is presented. This article contains brief descriptive discussions of the key physical features of all new algorithms and theoretical models, together with sample calculations that illustrate their performance.
Journal of physics. Condensed matter : an Institute of Physics journal, 2018
QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The p...
The Journal of Chemical Physics, 2004
In this work we introduce an electron localization function describing the pairing of electrons in a molecular system. This function, called ''electron pair localization function,'' is constructed to be particularly simple to evaluate within a quantum Monte Carlo framework. Two major advantages of this function are the following: ͑i͒ the simplicity and generality of its definition; and ͑ii͒ the possibility of calculating it with quantum Monte Carlo at various levels of accuracy ͑Hartree-Fock, multiconfigurational wave functions, valence bond, density functional theory, variational Monte Carlo with explicitly correlated trial wave functions, fixed-node diffusion Monte Carlo, etc͒. A number of applications of the electron pair localization function to simple atomic and molecular systems are presented and systematic comparisons with the more standard electron localization function of Becke and Edgecombe are done. Results illustrate that the electron pair localization function is a simple and practical tool for visualizing electronic localization in molecular systems.
PSI3: An open-sourceAb Initio electronic structure package
Journal of Computational Chemistry, 2007
PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistentfield, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License.
NCImilano : an electron-density-based code for the study of noncovalent interactions
Journal of Applied Crystallography, 2013
NCImilano, a Fortran90 code for applying the reduced density gradient (RDG) descriptor to a real-space study of noncovalent interactions, is presented. This code has been specifically designed for the X-ray charge density community, as it can deal with both gas-phase and solid-state electron densities as evaluated by popular multipolar (XD2006) and Gaussian-based quantum mechanical (Gaussian03/09, CRYSTAL) computational platforms. Moreover, it implements for the first time the possibility of plotting energy densities over RDG isosurfaces.