DensToolKit 2.0 (DTK) is now available!

DensToolKit2 is a versatile open-source, cross-platform, suite of programs for analyzing electronic densities calculated from various sources and getting cool plots for some of the most popular scalar fields out there, such as electron densities, spin densities, visualizing critical points, or investigating complex topologies of noncovalent interactions, DensToolKit2 provides an integrated, script-friendly suite for analyzing electron densities from *.wfx (wave function) files.

First developed at the "Benemérita University of Puebla, Mexico, by Profs. Juan Manuel Solano-Altamirano and Julio Manuel Hernández-Pérez, it has now incorporated various new workflows, including V_S,max based calculations of pKa and pkb as we've previously published.

To get the most out of DTK-v2, you want install the following programs before compiling DensToolKit-v2: gnuplot, povray, epstool, GraphicsMagick, and epstopdf.

~$sudo apt install gnuplot-qt
~$sudo apt install povray graphicsmagick epstool texlive-font-utils

Maybe also sudo apt install git. After installing git, clone the repository:

~$git clone https://github.com/jmsolano/denstoolkit

Once you've cloned the repository, you're almost ready to work with DTK. Move to the Downloads directory and into the denstoolkit directory in order to finish the installation, but first, lets check the available cpus with which we can work in order to make the most out your DTK experience. Check how many physical cores do you have available with the lscpu command (below, only a short section of the output is shown as an example):

~$lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Address sizes: 39 bits physical, 48 bits virtual
Byte Order: Little Endian
CPU(s): 12
On-line CPU(s) list: 0-11
Vendor ID: GenuineIntel
Model name: Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
CPU family: 6
Model: 165
Thread(s) per core: 2
Core(s) per socket: 6
Socket(s): 1
Stepping: 2
CPU(s) scaling MHz: 17%
CPU max MHz: 5000.0000
CPU min MHz: 800.0000
BogoMIPS: 5199.98

Look for the line that contains Core(s) per socket and Socket(s). The number of physical cores is (Core(s) per Socket) times (Socket(s)). In my computer, there are only six physical cores. The physical number of cores (even when the lscpu command would show 12 cpus, these are virtual cpus) is the maximum number of cores that can be effectively used for performing calculations. After this, move to the src directory and start the installation (recall that we are already in the Downloads/denstoolkit directory)

~$cd src 
~$make SETDTKNPROC=6 -j 4
~$sudo make install

The flags '-j 4' makes use of 4 cores to speed up the installation process; you may use all you've found with nproc if you're in a hurry. SETDTKNPROC=6 will produce the parallel version of DTK; each DTK program will use 6 cores to perform calculations.

To start working with DTK you may use the example wave function files located at:

~Downloads/denstoolkit/wffiles

Let's try obtaining an NCI (non-covalent interactions) plot, one of the most popular scalar fields available, using the H₂O dimer file named h2oh2o.wfx at the location above:

~$dtkgetnciplot -w h2oh2o.wfx -L -S 100 -l rdbu

All dtkXXX programs have the -h option which displays the various control options for each program. For dtkgetnciplot, -S ln uses a smart cuboid for the grid, where ln is the number of points in the direction of the largest axis (and in this case it is set to 100); -l defines the color palette to be used (in this case rdbu, but it could be viridis, or magma, among others, but you can import other palettes from the gnuplot github project)

Let's try another quick example. This time, to produce a heat map of the electron density of benzene, over the plane that contains the ring:

~$dtkplane benzene.wfn -n 100 -P -k -c -a 1 5 3 -h

Here, for dtkplane, -P creates a plot, -k Keeps the *.gnp file to be used later by gnuplot if needed, -c adds contour lines in the plot, and finally, -a 1 5 3 indicates the three atoms which define the plane to be plotted.

More posts on DTK to come, including the use of the all-new GUI! Please cite it as: Solano-Altamirano, J. M., Hernández-Pérez, J. M., Sandoval-Lira, J., & Barroso-Flores, J. (2024). DensToolKit2: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields. The Journal of Chemical Physics, 161(23). https://doi.org/10.1063/5.0239835