The LDD suite computes atomic contributions to the London dispersion energy and the dispersion density. It is based on the Atomic Decomposition of London Dispersion energy (ADLD) method and includes the following tools:

• lddensity.py – computes atomic dispersion contributions using the selected Grimme's dispersion correction and generates a .cube file with the London dispersion density function.
• PubQualityVMD.tcl – VMD script to automatically set visualization parameters for publication-quality images.

• Tools Description
• Requirements
• Usage
• Arguments Description
• Generate Only the Cube File
  • Dispersion Density Difference
• Renderings
• Credits
• License
• Contacts

Python script to compute atomic contributions to the London dispersion energy and the London dispersion density function using D3 or D4 corrections.

• Input:
  • {basename}.xyz : a classic .xyz file containing atomic coordinates of the system in ångström.
• Output:
  • .d3atomwise.txt or .d4atomwise.txt : a file containing atomic coordinates of the system with an additional column indicating each atom contribution to the London dispersion energy.
  • .d3out.txt or .d4out.txt : the original output generated by Grimme's DFT-D3 or DFT-D4 executable, respectively.
  • .d3omega.cube or .d4omega.cube : a .cube file that stores volumetric data of the LDD function, which can be used to easily visualize atomic contributions to London dispersion.

Script designed to visualize LD density function from a .cube file, adjusting VMD settings to generate publication-quality images.

• Python 3.x with standard libraries.
• For lddensity.py, ensure that .xyz file and the respective DFT-D3 or DFT-D4 executable are in the current path. The executable can be downloaded from the official website.
• For London dispersion density difference ensure {basename}.atomwise.txt is in the current path. See Dispersion Density Difference section for more information.
• VMD must be installed for running PubQualityVMD.tcl (download).

1. Ensure {basename}.xyz file is at the current path.

2. Run the script:

   python3 lddensity.py <basename> [-h] [--d {3,4}] [--npoints NPOINTS] [--func FUNC] [--damp DAMP] [--nprocs NPROCS] [--charge CHARGE]
                    [--s9 S9] [--onlycube]

1. Ensure the input .cube file you want to visualize is correctly named and located within an accessible directory (it's recommended to work within a single directory).

2. Edit the script with your favorite text editor to include the path name in set file_name command.

3. Run the script with the following command:

   vmd -e PubQualityVMD.tcl

Below is a detailed table of the arguments that can be used with our script. Each entry provides you with the name of the argument, a brief description, information on whether the argument is optional, and the default value it takes if not specified by the user. This table is designed to help you quickly understand how to configure the script to meet your specific requirements.

If you have already computed the atomic contributions (for example using another software), or if you want to plot the dispersion density difference function, you can use the --onlycube flag in lddensity.py.

In this case, the input file is not a standard .xyz, but rather an .xyz file with an extra column containing the atomic dispersion contributions in kcal/mol.
The file must be named {basename}.atomwise.txt, which corresponds to the file produced by the script when the --onlycube flag is not used.

An example of .atomwise.txt file for the $C_6H_6–Li$ system is:

#
atom   x(Å)         y(Å)        z(Å)        Edisp(kcal/mol)
C      -2.378672     1.005050   -0.079453   -2.128400
C      -2.318663    -0.385217   -0.085888   -2.128400
C      -1.085955    -1.028059   -0.147588   -2.128400
C       0.086589    -0.280636   -0.203051   -2.128300
C       0.026549     1.109641   -0.196866   -2.127300
C      -1.206135     1.752463   -0.134993   -2.127300
H      -3.337288     1.505059   -0.038209   -0.486950
H      -3.230736    -0.966137   -0.050005   -0.487450
H       0.937922     1.690612   -0.246784   -0.486450
H      -1.253275     2.833395   -0.136867   -0.486550
H      -1.039495    -2.108952   -0.159689   -0.487350
H       1.044500    -0.780664   -0.258085   -0.486850
Li     -1.018560     0.350445    2.545363   -3.707400

To generate the dispersion density difference between two molecular systems:

1. Compute the atomic dispersion contributions for both systems separately.
2. Be sure there's an atom-to-atom mapping between the two structures.
3. Build a new {basename}.atomwise.txt file where the atomic dispersion contribution for each atom corresponds to the difference between its values in the two systems.
4. Use this difference file as input to generate the .cube file with --onlycube.

This procedure allows you to visualize the difference between atomic LD contributions for two different molecular structures (e.g., a pair of structures along a reaction profile).

An example command could be:

python3 lddensity.py system_diff --onlycube --npoints 80 --nprocs 2

The image below is a rendering generated with PubQualityVMD.tcl for a $C_6H_6–Li$ system. Red/blu color indicates high/low atomic dispersion contribution.

If you use the LDD suite in your research or any publication, please cite:

• https://pubs.acs.org/doi/full/10.1021/acscentsci.5c00356

• https://pubs.acs.org/doi/abs/10.1021/acs.jctc.3c00977

• https://github.com/bistonigroup/LDDsuite

Distributed under GNU Lesser General Public License with restrictions. See LICENSE for more information.

For general inquiries, feedback, or assistance with using the LDD suite, please contact us at:

Gianluca Regni - gianluca.regni@dottorandi.unipg.it
Lorenzo Baldinelli - lorenzo.baldinelli@dottorandi.unipg.it
Giovanni Bistoni - giovanni.bistoni@unipg.it