FretLab: an Open Source Code for Electronic Energy Transfer Computation

Table of Contents

• About
• Installation
• Usage
• Publications
• License
• Contact

About

FretLab is a high-performance computational tool designed to compute electronic energy transfer (EET) rates. It supports three general use cases:

1. Donor to acceptor chromophore EET
2. Plasmonic substrate to acceptor chromophore EET
3. Donor to acceptor chromophore EET mediated by a plasmonic substrate

FretLab is designed for speed and scalability using parallel processing with OpenMP and efficient linear algebra routines.

Theoretical Framework

All quantities in FretLab are expressed in atomic units. The EET rate is calculated using Fermi’s Golden Rule:

$$ \kappa_{\text{EET}} = \frac{2\pi}{\hbar} \ |V|^2 \ J $$

Where:

• V is the total coupling potential between donor and acceptor
• J is the spectral overlap integral

In the presence of a plasmonic substrate (modeled via induced charges $$q_k$$ and, if applicable, induced dipoles $$\mu_k$$), the total coupling V becomes:

$$ V = V_{\text{coulomb}} \ + V_{\text{overlap}} \ + V_{\text{environment}}^{\text{ q}} + V_{\text{environment}}^{ \mu} $$

$$ V_{\text{coulomb}} = \int d\mathbf{r} \ d\mathbf{r'} \ \frac{\rho_A^*(\mathbf{r}) \rho_D(\mathbf{r'})}{|\mathbf{r} - \mathbf{r'}|} $$

$$ V_{\text{overlap}} = - \omega_0 \int d\mathbf{r} \ d\mathbf{r'} \ \rho_A^*(\mathbf{r}) \rho_D (\mathbf{r'}) $$

$$ V_{\text{environment}}^{\text{ q}} = \sum_k \left( \int d\mathbf{r} \ \frac{\rho_A^*(\mathbf{r})}{|\mathbf{r} - \mathbf{r}_k|} \right) q^\omega(\mathbf{r}_k; \rho_D) $$

$$ V_{\text{environment}}^{\mu} = \sum_k \left( \int d\mathbf{r} \ -\frac{\mathbf{r} - \mathbf{r}_k}{|\mathbf{r} - \mathbf{r}_k|^3} \cdot \rho_A^*(\mathbf{r}) \right) \mu^\omega(\mathbf{r}_k; \rho_D) $$

Where:

• $\rho_A$ and $\rho_D$ are the acceptor and donor charge densities
• $\omega_0$ is the incident frequency
• $q_k^\omega(\mathbf{r}_k; \rho_D)$ are the frequency-dependent induced charges at positions $\mathbf{r}_k$
• $\mu_k^\omega(\mathbf{r}_k; \rho_D)$ are the frequency-dependent induced dipoles at positions $\mathbf{r}_k$

Installation

FretLab requires the following dependencies:

• CMake 3.14 or higher
• Python 3.8+
• Fortran compiler (gfortran 9.3.0 or higher recommended)
• LAPACK/BLAS libraries (MKL suggested)
• Python runtest module (pip install runtest)
• OpenMP support

If using MKL (recommended), set the following environment variable:

export MATH_ROOT=/opt/intel/mkl/lib/intel64_lin

Compilation

To build FretLab, run:

./setup.sh -omp -fc <fort-path>

cd build/
make

This will generate an executable named FretLab inside the build/ directory.

Options:

• -omp : Enables OpenMP (recommended)
• -fc <fort-path> : Path to the Fortran compiler (optional)

Running Tests:

After building, you can run the test suite with:

cd build/
ctest

Usage

To execute a simulation, run:

./FretLab input_file.inp

To see example input files and different configuration options, refer to the files located in:

tests/

Publications

FretLab has been used in the following research paper(s):

• Grobas Illobre, P.; Sodomaco, S.; Lafiosca, P.; Giovannini, T.; Cappelli, C. The Role of Atomistic Tip Morphology in Tip-Enhanced Electronic Energy Transfer. Nano Lett. 2026. https://doi.org/10.1021/acs.nanolett.6c03248

License

FretLab is licensed under the GNU General Public License v3.0.

Acknowledgments & Funding

This project has been supported by the FARE 2020 program — "Framework per l’attrazione e il rafforzamento delle eccellenze per la ricerca in Italia."

FretLab has been developed as part of a collaborative scientific effort involving Tommaso Giovannini, Piero Lafiosca, Sveva Sodomaco, and Chiara Cappelli.

Contact

For issues or contributions:

• Email: pgrobasillobre@gmail.com
• Github issues: https://github.com/pgrobasillobre/FretLab/issues