Dataset for "Ultra-strong coupling of a single molecule to a plasmonic nanocavity: A first-principles study"

# Data and code for "Ultra-strong coupling of a single molecule to a plasmonic nanocavity: A first-principles study," M. Kuisma, B. Rousseaux, K.M. Czajkowski, T.P. Rossi, T. Shegai, P. Erhart, T.J. Antosiewicz, ACS Photonics, doi:10.1021/acsphotonics.2c00066 (2022). <br> ## Contents * *data-{type}/*: reproducible data<br> * *src/*: input scripts <br> ## Description of the data The data are stored in directories *data-{type}/*. The contents of the directories<br> can be reproduced with the included input scripts. The data are organized in subdirectories *data-{type}/{system}/* corresponding to<br> the considered nanoparticle-molecule systems and simulation type: * data-fd: free energy calculations done with the finite difference mode<br> * data-lcao: strong coupling calculations done with LCAO mode<br> * data-d3: DFT-D3 calculations The contents of each subdirectory are: * *data-{fd,lcao,d3}/{system}/structure.xyz*: physical atomic structure<br> * *data-lcao/{system}/td-x/dm.dat*: delta-kick-induced time-dependent dipole moment<br> * *data-lcao/{system}/td-x/dm_abs_Lorentz_0.100.dat*: photoabsorption spectrum The spectrum plots in the article correspond to the first (x values) and<br> second (y values) columns of the spectrum files. ## Reproduction of the data The data was produced using the Python scripts in *src/*,<br> Python version 3.7.3, GPAW version 20.1.0, libxc version 4.3.4,<br> ASE version 3.20.0, NumPy version 1.16.2, and SciPy version 1.2.1. The calculation of the data of a system consists of<br> the following steps (in *bash* shell with, e.g., system=rlx-ico-Al147`): 1. Ground-state calculation:<br> * Copy the gs folder to a data-lcao/{system} folder<br> * Set up parellel calculaton parameters as necessary for the computing infrastructure (parallel.py)<br> * Select the Poisson Solver in the settings.py file by commenting out / uncommenting:<br> * for single particles or molecules use poissonsolver = PoissonSolver(eps=eps, remove_moment=9)<br> * otherwise comment out the above line and uncomment the last 8 lines<br> * Submit the gs.py calculation as appropriate for the particular system<br> 2. Time-propagation calculation:<br> * Requires finished ground-state calculation<br> * Set up parellel calculaton parameters as necessary for the computing infrastructure (parallel.py)<br> * Submit the td.py calculation as appropriate for the particular system<br> 3. Spectrum calculation:<br> * Requires finished time-propagation calculation (30 fs propagation)<br> * Run the `$ python spec.py` script Note that the example python scripts use variables STARTTIME and WALLTIME to define<br> allocated compuing time in HPC environments. The `WALLTIME` and `STARTTIME` environment<br> variables defined in *submit.sbatch* are required for a clean exit of the calculation<br> within the allocated time. If the ground-state or time-propagation calculations do not finish within the<br> allocated time, the same *gsc.py* or *tdc.py* scripts can be (re)run to continue<br> the calculation.