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Here you can find some plots and figures created from data obtained using DensToolKit. If you would like to use the software, please visit the following websites, according to your preferences. For the scientific 2015 paper, please visit http://dx.doi.org/10.1016/j.cpc.2015.07.005, and for the 2024 paper visit https://doi.org/10.1063/5.0239835. For downloading the suite, please visit the official Comput. Phys. Comm. program library website (http://www.cpc.cs.qub.ac.uk), or the github repository (https://github.com/jmsolano/denstoolkit).
Should you want the most recent (beta) version of DensToolKit, please write me an e-mail (jmsolanoalt at gmail dot com). Also, we kindly ask for your support by e-mailing us about using DTK: i.e., if you used it and liked it, just let us know. In this manner, we can increase the time devoted to developing DensToolKit.
Some publications wherein we have successfully used DensToolKit are:
A. Ramírez-Sánchez, P. Amador, K. Salas-López, Julio M. Hernández-Pérez, J.M. Solano-Altamirano, "Experimental and computational thermochemical study of three hydroxy-substituted phthalimides", Jour. Chem. Thermodyn., 174 (2022) 106862.
L. Monterrosas-Pérez, J. Sandoval-Lira, M. P. Amador-Ramírez, H. Flores-Segura, Julio M. Hernández-Pérez, J. M. Solano-Altamirano, Struct. Chem. (2019).
J. M. Ledo, H. Flores, J. M. Solano-Altamirano, F. Ramos, J. M. Hernández-Pérez, E. A. Camarillo, B. Rabell, M. P. Amador, Jour. Chem. Thermodyn. (2018).
J. M. Ledo, H. Flores, J. M. Hernández-Pérez, F. Ramos, E. A. Camarillo and J. M. Solano-Altamirano, Jour. Chem. Thermodyn., 116 (2018) 176 - 184.
S. Mejía, Julio M. Hernández-Pérez, J. Sandoval-Lira, and F. Sartillo-Piscil, Molecules, 22(3) (2017) 361.
J. Sandoval-Lira, M. Hô, R. Hernández-Esparza, J. C. Ramírez, Julio M. Hernández-Pérez, Theor. Chem. Acc., 135 (2016) 149.
DensToolKit version 2, currently compiles with gcc under Linux (tested on fedora and ubuntu), MacOSX (tested on Snow-Leopard and Mountain Lion, and also on M1 Apple Silicon chips), and Windows (through cygwin, tested on Windows 7). For complete functionality, it is recommended to install gnuplot, epstopdf, epstool, GraphicsMagick, and PovRay. These programs are used for rendering plots and figures, however they are not required to produce the chemical data.
The input files for this suite are the wave function files, either in the old wfn format or in the more versatile format wfx (the cool program Molden2Aim can convet molden format to wfx, which increases the compatibility of DensToolKit with other Quantum Chemistry programs). DensToolKit's output can be dat, tsv (tab-separated values), or Gaussian cub formats. For dat files, we use the conventions adopted by gnuplot (if a line starts with the character '#', it is considered a comment, thus it is skipped). Also, we follow the conventions of gnuplot for tsv files (each block of data is separated by an empty line).
For storing the critical points information, we use a format inspired in the wfx format (actually we called it 'cpx' format). And the diagrams (such as the ones shown in the last figures of this webpage) can be obtained using povray (the same program used for finding the critical points provides the pov file).
In the last version, we have added a viewer (DTKViewer), which can be compiled in Linux and MacOSX. A precompiled version for MacOSX can be found here. Further instructions on compiling the viewer can be found in the git repo. This viewer is experimental and it works as part of the DTK workflow (i.e. it is best exploited if you use it as a fast-visualization tool, as opposed to use it to render images of the critical point maps per se). It is ideal to choose a final view of a molecule, and pass the angles to the pov file, which yields images of greater quality.
LOL of cyclopropane molecule. The LOL density is shown in the plane passing through the three Carbon atoms. This image was rendered with gnuplot, epstool, and GraphicsMagick.
First order density matrix of the cyclopropane molecule. The density matrix is mapped using the bond path between two Carbon atoms. The image was rendered using gnuplot, epstool, and GraphicsMagick.
All the electron density critical points [CP] (Nuclear CP, Bond CP, and Ring CP) of the cyclopropane molecule. This image was rendered using povray. The script for povray is generated by the same program that finds the critical points. The green dots depict the bond path between Nuclear CP and Bond CP. Transparent spheres represent atoms.
All the electron density critical points [CP] (Nuclear CP, Bond CP, and Ring CP) of the ethane molecule. This image was rendered using povray. The script for povray is generated by the same program that finds the critical points. The green dots depict the bond path between Nuclear CP and Bond CP. Transparent spheres represent atoms.
All the electron density critical points [CP] (Nuclear CP, Bond CP, and Ring CP) of the cubans molecule. This image was rendered using povray. The script for povray is generated by the same program that finds the critical points. The green dots depict the bond path between Nuclear CP and Bond CP. Transparent spheres represent atoms.
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