Dynemol

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DynEMol: tools for studying Excited State Dynamics of Electrons in Molecules

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# Dynemol

Tools for studying Dynamics of Electrons in Molecules

DynEMol: Dynamics of Electrons in Molecules DynEMol is an open-source suite for simulating nonadiabatic excited-state dynamics and molecular systems using a hybrid semiempirical approach. It has been in continuous development since 2013 and is actively maintained.

DynEMol combines two computational strategies:

Extended Hückel theory for the electronic structure

Classical force fields (AMBER/OPLS-compatible) for nuclear motion

This allows it to model a wide range of systems with nonadiabatic dynamics, including:

Molecules in vacuum or solution

Molecule–solid and solid–liquid interfaces

Bulk (crystalline and disordered) materials

## Features

- Excited-state nonadiabatic dynamics (Ehrenfest, FSSH, Ehrenfest-CSDM, and propagation in diabatic basis)
- Classical molecular dynamics
- Geometry optimization
- Force-field and extended-Hückel parameter optimization
- Time-dependent electron and hole population analysis
- Electronic and vibronic density of states (DOS, VDOS)
- Pre- and post-processing tools for simulations and analysis

## Optimizations

Parallelization & Branches:

The repository is divided into two main branches:

- master — optimized for HPC clusters with MPI + OpenMP support and some GPU acceleration

- SingleNode — optimized for single-node systems, parallelized with OpenMP and supports the same GPU routines

Both branches include a folder name manipulate/ containing standalone utilities for:

- Editing input structures (copy, rotate, translate, delete atoms)
- Pre- and post-processing tools for simulations and analysis
- Generating plots from simulation output (/manipulate/general.util)

## Input & File Formats

DynEMol supports a range of input formats:

- Coordinates: .pdb

- Force fields: AMBER/OPLS-compatible .psf, .prm, .itp, .top

- Configuration files: card.inpt, velocity.inpt, opt_eht_parms.inpt

Input file specifications can be found in:

card_file_formats

IO_file_formats

IO_file_MM-formats

cost_file_formats

## Installation

Code & Compilation:

DynEMol is primarily written in Modern Fortran (2003/2008/2018) and is designed to work best with Intel compilers:

- Use make-ifx for Intel oneAPI (LLVM-based compilers)

- Use make-ifort for legacy Intel compilers (pre-2022)

Other compilation targets (e.g., for debugging or profiling) are documented in the makefile.

To compile:

```bash
cp make-ifx makefile  # or make-ifort, depending on your compiler
make
```
    
To run this project, you will need to add the following environment variables to your .env file

```bash
export DYNEMOLDIR=/path/to/dynemol
export DYNEMOLWORKDIR=$(pwd)

# Place your input files in $DYNEMOLWORKDIR
$DYNEMOLDIR/dynemol
```

`Execution Script`: run-dynemol.sh

The script `run-dynemol.sh` is a convenience wrapper for running DynEMol simulations. It handles environment setup and execution in a consistent way.

To make it accessible from anywhere in your terminal, place the script in your $HOME/bin directory:
```bash
mkdir -p $HOME/bin
cp run-dynemol.sh $HOME/bin/
chmod +x $HOME/bin/run-dynemol.sh
```
Make sure $HOME/bin is in your PATH (add this to your .bashrc or .zshrc if it’s not already):
```bash
export PATH=$HOME/bin:$PATH
```
Once configured, you can run DynEMol from any project directory with:
```bash
run-dynemol.sh
```
This will execute the simulation using the input files located in the current working directory.
Outputs will be saved in folders such as dyn.trunk/, dos.trunk/, MO.trunk/, etc., and refreshed at each execution.

## Authors

- [@lgcrego](https://www.github.com/lgcrego)

Contributors:
- [@roboliboni](https://github.com/roboliboni)
- [@albertotrj](https://github.com/albertotrj)

If you have questions or encounter issues, feel free to open an issue on this GitHub repository or contact the maintainer directly at luis.gc.rego [at] gmail.com.

## Reference this project:

- Oliboni, R. S.; Bortolini, G.; Torres, A.; Rego, L. G. C. A nonadiabatic excited state molecular mechanics/extended Hückel Ehrenfest method. J. Phys. Chem. C 2016, 120, 27688–27698.
- Torres, A.; Prado, L. R.; Bortolini, G.; Rego, L. G. C. Charge Transfer Driven Structural Relaxation in a Push–Pull Azobenzene Dye–Semiconductor Complex. J. Phys. Chem. Lett. 2018, 9, 5926–5933
- Rego, L. G. C.; Bortolini, G. Modulating the Photoisomerization Mechanism of Semiconductor-Bound Azobenzene-Functionalized Compounds. J. Phys. Chem. C 2019, 123, 5692–5698.
- D. A. Hoff and L. G. C. Rego, “Chirality-induced propagation velocity asymmetry,” Nano Letters, vol. 21, no. 19, pp. 8190–8196, 2021.

## Screenshots

![App Screenshot](http://luisrego.sites.ufsc.br/wp-content/uploads/2017/12/perylene-structure-152x300.png) 
![App Screenshot](http://luisrego.sites.ufsc.br/wp-content/uploads/2017/12/interface-274x300.png) 
![App Screenshot](http://luisrego.sites.ufsc.br/wp-content/uploads/2016/03/el_dos_occ_smear-7-300x214.png)

## Acknowledgements

- [SDumont](https://sdumont.lncc.br/)
 - [CENAPAD-SP](https://www.cenapad.unicamp.br/)
 - [NACAD](https://portal.nacad.ufrj.br/)

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