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).

## Contents

* *data-{type}/*: reproducible data
* *src/*: input scripts

## Description of the data

The data are stored in directories *data-{type}/*. The contents of the directories
can be reproduced with the included input scripts.

The data are organized in subdirectories *data-{type}/{system}/* corresponding to
the considered nanoparticle-molecule systems and simulation type:

* data-fd: free energy calculations done with the finite difference mode
* data-lcao: strong coupling calculations done with LCAO mode
* data-d3: DFT-D3 calculations

The contents of each subdirectory are:

* *data-{fd,lcao,d3}/{system}/structure.xyz*: physical atomic structure
* *data-lcao/{system}/td-x/dm.dat*: delta-kick-induced time-dependent dipole moment
* *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
second (y values) columns of the spectrum files.

## Reproduction of the data

The data was produced using the Python scripts in *src/*,
Python version 3.7.3, GPAW version 20.1.0, libxc version 4.3.4,
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
the following steps (in *bash* shell with, e.g., system=rlx-ico-Al147`):

1. Ground-state calculation:
    * Copy the gs folder to a data-lcao/{system} folder
    * Set up parellel calculaton parameters as necessary for the computing infrastructure (parallel.py)
    * Select the Poisson Solver in the settings.py file by commenting out / uncommenting:
        * for single particles or molecules use poissonsolver = PoissonSolver(eps=eps, remove_moment=9)
        * otherwise comment out the above line and uncomment the last 8 lines
    * Submit the gs.py calculation as appropriate for the particular system
2. Time-propagation calculation:
    * Requires finished ground-state calculation
    * Set up parellel calculaton parameters as necessary for the computing infrastructure (parallel.py)
    * Submit the td.py calculation as appropriate for the particular system
3. Spectrum calculation:
    * Requires finished time-propagation calculation (30 fs propagation)
    * Run the `$ python spec.py` script

Note that the example python scripts use variables STARTTIME and WALLTIME to define
allocated compuing time in HPC environments. The `WALLTIME` and `STARTTIME` environment
variables defined in *submit.sbatch* are required for a clean exit of the calculation
within the allocated time.

If the ground-state or time-propagation calculations do not finish within the
allocated time, the same *gsc.py* or *tdc.py* scripts can be (re)run to continue
the calculation.