TopChem2 Cube is specifically designed code for the topological analysis from three-dimensional cube grids link1 link2 of both the electron density and/or the electron localization function (ELF). Typically, the 3D grids are output files directly obtained from a quantum chemistry code (see below). The program makes use of a full algorithm enabling to numerically assign the data points grids to basin volumes. It is distributed as binairies, free of charge.
Easily usable in command-line or via a Graphical User Interface written in Python3, automatic and robust.
by J. Pilmé, Laboratoire de Chimie Théorique - Sorbonne Université
Using TopChem2 Cube requires agreement to the following conditions upon receipt of the program:
I understand that copyright and intellectual
property rights are retained by the author
I am allowed to supply a copy of the
code to anyone. In this case I will inform the author.
I agree to use this sotware for no profit
I will not incorporate any part of
the code in a commercial software
New Insights in Quantum Chemical Topology Studies Using Numerical Grid-based Analyses D. Kozlowski and J. Pilmé , J. Comput. Chem. 32, Issue 15, pages 3207–3217, 2011
Some topological analysis references in no specific order
An efficient method for computing the QTAIM topology of a scalar field: The electron density case
J. I. Rodriguez, J. Comput. Chem., 34, pp. 681–686, 2013
Classification of chemical bonds based on topological analysis of electron localization functions
B. Silvi and A. Savin. Nature, 371, pp. 683–686, 1994
Computational tools for the electron localization function topological analysis
S Noury, X Krokidis, F Fuster, B Silvi. Computers & chemistry, 23 (6), pp. 597-604, 1999
Topological analysis of the electron localization function applied to delocalized bonds
A Savin, B Silvi, F Colonna. Canadian journal of chemistry, 74 (6), pp. 1088-1096, 1996
Determination of the electron localization function from electron density
V. Tsirelson and A. Stash. Chem. Phys. Lett. 351 (1-2), pp. 142-148, 2002
Subshell Fitting of Relativistic Atomic Core Electron Densities for Use in QTAIM Analyses of ECP-Based Wave Functions Todd A. Keith and Michael J. Frisch, J. Phys. Chem. A, 115, pp. 12879-12894, 2011
Advancing beyond Charge Analysis using the Electronic Localization Function: Chemically Intuitive Distribution of Electrostatic Moments. J. Pilmé and J-P Piquemal. J. Comput. Chem., 29(9), pp. 1440-1449, 2008
Input files TopChem2 Cube
Input files of TopChem2 are 3D cube files generated by quantum chemistry codes, typically:
- Gaussian: link ; use the utility cubegen for generating cubes files.
Several output files of TopChem2 can be processed by advanced free visualization code such as Molekel ,
VMD or VESTA programs. They can be used for rendering plots but they are not required to compute and produce chemical data.
All Critical points for the electron density and all attractors for the electron localization function (included the degenerated attractors circular and spherical). Numerous descriptors computed at critical points locations are printed:
Electron localization function
Laplacian of the electron density
Gradient norm of the electron density and ELF
Eigenvalues of hessian matrix
Basin and Population Analysis
TopChem2 looks for all basins of the gradient scalar field along the descent trajectories from attractor points. The algorithm is similar to the one used by the TopMod program [Computers & chemistry, 23 (6), pp. 597-604, 1999]. Each grid point is assigned to a basin volume, assignment codes are stored in an array.
Top Left : Basin isosurface of the electron localization function obtained from a CPMD Wannier snaphot. Top Right : Process of points' assignment to basins.
Bottom left : basin isosurface of the electron density for a water ice cell obtained from VASP CHGCAR file after being converted to cube file (vasp_to_cube utility) .
Bottom right: All the electron density critical points of the orthonitrophenol molecule.
Atomic charges, basin ELF populations and dipole & quadrupole moments are also computed. Atomic contributions to ELF populations.
Graphical User Interface: A basic GUI written in python3 is included in the package for setting up and running calculations with topchem2_cube.
System requirements : Linux (GLIBC 2.4 or later), Intel/AMD (x86) processor(s), 64 bit & 32 bit
GUI librairies requirements : tkinter, numpy and matplotlib.