TopChem2 Cube is specifically designed code for the topological analysis from only three-dimensional cube grids link1 link2 of the electron density/the electron localization function (ELF)/the Molecular Electrostatic Potential (MEP) function. 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
contact email: pilme@lct.jussieu.fr

Read the user manual: Starting with TopChem2 Cube

Licence agreement

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 purpose
  • I will not incorporate any part of the code in a commercial software

Citation

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.

- Molpro: link

- NWChem: link

- Dalton (documentation p. 303) : link

- Turbomole: link

- Octopus: link

-DFTB+ (Waveplot Program): link

- VASP: link ; CHGCAR and ELFCAR files can be directly used for generating cube files using the utility vasp_to_cube included in the TopChem2 Cube package.

- CPMD: link ; use the utility cpmd2cube for generating cubes files.

- Crystal (documentation p. 401): link

- Quantum Espresso: link

- ADF: link

- CP2K: link

This list does not pretend to be exhaustive. ..

Calculation Features

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 density
    Electron localization function
    Laplacian of the electron density
    Gradient norm of the electron density and ELF/MEP
    Eigenvalues of hessian matrix
    Energy densities
    Ellipticity
    Bond metallicity
    Shannon entropy
    Local temperature
    ...

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.

NCO
 
chgcar ice

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/MEP populations and dipole & quadrupole moments are also computed. Atomic contributions to ELF/MEP populations.

 

Visualization Feature

Graphical User Interface: A basic GUI written in python3  is included in the package for setting up and running calculations with topchem2_cube.

Download

System requirements : Linux (GLIBC 2.4 or later), Intel/AMD (x86) processor(s), 64 bit

GUI librairies requirements : tkinter, numpy and matplotlib.

TopChem2 Cube 64-bit: Download

Installation:

A. Open a linux terminal and extract the files from the tar archive:

             > tar -xvf TopChem2_cube64.tar.gz

B. Change the directory to where the files are located:

             > cd INSTALL_TOPCHEM64

C. Run the bash script installer, it does not require administrative privileges to run:

            >  bash installer.sh

 

Last updated on July, 2018.