ORBKIT: A modular python toolbox for cross‐platform postprocessing of quantum chemical wavefunction data

ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wavefunction, as well as several grid‐independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by user‐written modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT possesses routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is open‐source under GNU‐LGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations. © 2016 Wiley Periodicals, Inc.

[1]  Stefan Behnel,et al.  Cython: The Best of Both Worlds , 2011, Computing in Science & Engineering.

[2]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[3]  Gunter Hermann,et al.  Laser-Driven Hole Trapping in a Ge/Si Core–Shell Nanocrystal: An Atomistic Configuration Interaction Perspective , 2015 .

[4]  Alan Genz,et al.  An adaptive algorithm for numerical integration over an n-dimensional rectangular region , 1980 .

[5]  Eric Jones,et al.  SciPy: Open Source Scientific Tools for Python , 2001 .

[6]  Tian Lu,et al.  Bond order analysis based on the Laplacian of electron density in fuzzy overlap space. , 2013, The journal of physical chemistry. A.

[7]  Gaël Varoquaux,et al.  Mayavi: 3D Visualization of Scientific Data , 2010, Computing in Science & Engineering.

[8]  Tian Lu,et al.  Multiwfn: A multifunctional wavefunction analyzer , 2012, J. Comput. Chem..

[9]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[10]  T. H. Dunning.  Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .

[11]  Gaël Varoquaux,et al.  The NumPy Array: A Structure for Efficient Numerical Computation , 2011, Computing in Science & Engineering.

[12]  Frank Neese,et al.  The ORCA program system , 2012 .

[13]  Laurence D. Barron,et al.  Vibrational optical activity , 2010 .

[14]  Ronald J. Gillespie,et al.  Chemical Bonding and Molecular Geometry: From Lewis to Electron Densities , 1972 .

[15]  Jun Li,et al.  Basis Set Exchange: A Community Database for Computational Sciences , 2007, J. Chem. Inf. Model..

[16]  Marcus D. Hanwell,et al.  Avogadro: an advanced semantic chemical editor, visualization, and analysis platform , 2012, Journal of Cheminformatics.

[17]  Gunter Hermann,et al.  Imaging the Ultrafast Photoelectron Transfer Process in Alizarin-TiO2 , 2015, Molecules.

[18]  Richard F. W. Bader.  A quantum theory of molecular structure and its applications , 1991 .

[19]  Axel Schild,et al.  Electron Fluxes During Chemical Processes in the Electronic Ground State , 2013 .

[20]  Michael J. Frisch,et al.  Transformation between Cartesian and pure spherical harmonic Gaussians , 1995 .

[21]  Laurence A. Nafie.  Electron Transition Current Density in Molecules. 1. Non-Born−Oppenheimer Theory of Vibronic and Vibrational Transitions , 1997 .

[22]  F. Martín,et al.  Applications of B-splines in atomic and molecular physics , 2001 .

[23]  Laurence A. Nafie,et al.  Vibrational Optical Activity: Principles and Applications , 2011 .

[24]  L. Pacios,et al.  CheckDen, a program to compute quantum molecular properties on spatial grids. , 2009, Journal of molecular graphics & modelling.

[25]  Matthew L. Leininger,et al.  Psi4: an open‐source ab initio electronic structure program , 2012 .

[26]  David Feller.  The role of databases in support of computational chemistry calculations , 1996 .

[27]  Julia Contreras-García,et al.  Revealing noncovalent interactions. , 2010, Journal of the American Chemical Society.

[28]  Luis Fernández Pacios,et al.  Check Den: a computer program to generate 1D, 2D and 3D grids of functions dependent on the molecular ab initio electron density , 2003, Comput. Biol. Chem..

[29]  Terje O. Espelid,et al.  An adaptive algorithm for the approximate calculation of multiple integrals , 1991, TOMS.

[30]  Gunter Hermann,et al.  Electronic and nuclear flux densities in the H 2 molecule , 2014 .

[31]  Alán Aspuru-Guzik,et al.  Advances in molecular quantum chemistry contained in the Q-Chem 4 program package , 2014, Molecular Physics.

[32]  Juan Manuel Solano-Altamirano,et al.  DensToolKit: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields , 2015, Comput. Phys. Commun..

[33]  A. Szabó,et al.  Modern quantum chemistry : introduction to advanced electronic structure theory , 1982 .

[34]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[35]  Paul L. A. Popelier,et al.  Atoms in molecules , 2000 .

[36]  Chris Morley,et al.  Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.

[37]  F. Jensen.  Introduction to Computational Chemistry , 1998 .

[38]  Vincent Pohl,et al.  Adiabatic electronic flux density: A Born-Oppenheimer broken-symmetry ansatz , 2015, 1510.05785.

[39]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[40]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..

[41]  Beate Paulus,et al.  Electron density dynamics in the electronic ground state: motion along the Kekulé mode of benzene. , 2012, The journal of physical chemistry. A.

[42]  Paul L. A. Popelier,et al.  Atoms in Molecules: An Introduction , 2000 .

[43]  R. Bader.  Atoms in molecules : a quantum theory , 1990 .

[44]  Karsten W. Jacobsen,et al.  An object-oriented scripting interface to a legacy electronic structure code , 2002, Comput. Sci. Eng..

[45]  Tjerk P. Straatsma,et al.  NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations , 2010, Comput. Phys. Commun..

[46]  G. Schaftenaar,et al.  Molden: a pre- and post-processing program for molecular and electronic structures* , 2000, J. Comput. Aided Mol. Des..

[47]  Teresa B. Freedman,et al.  Electron Transition Current Density in Molecules. 3. Ab Initio Calculations for Vibrational Transitions in Ethylene and Formaldehyde , 1997 .

[48]  W. Marsden.  I and J , 2012 .

[49]  Sason Shaik,et al.  Topology of electron charge density for chemical bonds from valence bond theory: a probe of bonding types. , 2009, Chemistry.

[50]  P. Jeffrey Hay,et al.  Gaussian Basis Sets for Molecular Calculations , 1977 .

[51]  Noel M. O'Boyle,et al.  cclib: A library for package‐independent computational chemistry algorithms , 2008, J. Comput. Chem..

[52]  Lorenzo Avaldi,et al.  Observation of excited states of H2+ by threshold photoelectron spectroscopy , 1999 .