Non-adiabatic EXcited-state Molecular Dynamics (NEXMD)

nexmd.exe is a command-line Fortran90 program designed to understand the non-radiative relaxation of a main-block molecule with 100s of atoms and 10s of relevant excited states on the picosecond time scale after a vertical photoexcitation. With this design goal, nexmd.exe has implementations of various non-adiabatic molecular dynamics(NAMD) algorithms, with efficiency and stability improvements to reach these time scales. To provide the electronic structure parameters for these NAMD algorithms, nexmd.exe also performs the self-consistent electronic structure, linear response, quadratic response and 'Z-vector' calculations 'on-the-fly' ; using the CEO (collective electronic oscillator) package with semiempirical Hamiltonians from the SQM package. For the classical nuclei and Tully density matrix propagation, only the classical nuclear geometry, nuclear velocity and the Tully density matrix at $t=0$ (when the vertical excitation occurs) need be provided. NEXMD's modular design allows for individual calculations to be carried out with different control words in the input file, thus NEXMD is capable of calculating, among many possibilities, energy minimized geometries and absorption spectra, at the same level of theory as the NAMD.

NEXMD is a scientific program that assumes that the input it is given is worth running through its algorithms to give reproducible output.

There is a helper Python3 script getexcited.py to aid in the preparation of the input file, submission of a swarm of trajectories (parallelization) and processing the ouput (statistics and visualization), with a copy in this repository and a more frequently updated pypi package.

Highlighted Features

Solvation correction to the total energy for a single point nuclear geometry.
Sampling nuclear geometries of the ground-state potential energy surface (PES) under NVE or NVT (through Langevin dynamics).
Vertical excitation stick and broadened spectrum for a single point nuclear geometry or an ensemble of nuclear geometries.
Gaussian cube files for the transition density matrix and natural transition orbitals for a vertical excitation. (Relies on external scripts as of now. Integrate it?)
Minimum energy nuclear geometry and vibrational force constants on any calculated ground or excited state PES.
Born-Oppenheimer molecular dynamics trajectories on any calculated ground or excited state PES.
Non-adiabatic molecular dynamics trajectories following the algorithms of trajectory surface hopping (TSH), Ehrenfest, or ab-initio multiple cloning (AIMC).
Geometry constraints for all molecular dynamics simulations. Currently supports freezing bond distances or normal modes of the molecules.

Please refer to the NEXMD manual for a complete list of supported calculations.

How to cite

When using NEXMD results in academic work, please cite the package:

Walter Malone, Benjamin Nebgen, Alexander White, Yu Zhang, Huajing Song, Josiah A. Bjorgaard, Andrew E. Sifain, Beatriz Rodriguez-Hernandez, Victor M. Freixas, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Tammie R. Nelson, and Sergei Tretiak, NEXMD Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations, Journal of Chemical Theory and Computation 2020 16 (9), 5771-5783, DOI: 10.1021/acs.jctc.0c00248

as well as the 2020 review of the methods implemented in NEXMD:

Tammie R. Nelson, Alexander J. White, Josiah A. Bjorgaard, Andrew E. Sifain, Yu Zhang, Benjamin Nebgen, Sebastian Fernandez-Alberti, Dmitry Mozyrsky, Adrian E. Roitberg, and Sergei Tretiak, Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials, Chemical Reviews 2020 120 (4), 2215-2287, DOI: 10.1021/acs.chemrev.9b00447

we encourage users to cite the references and libraries used by NEXMD, which are detailed in the NEXMD manual.

Usage

Prerequisites

The following dependencies must be installed and configured before compiling nexmd.exe: (1) a build automation tool such as make, (2) a FORTRAN90 compiler, (3) and a BLAS/LAPack library compatible with the compiler and associated libraries.

Build automation tool

make is a standard tool

FORTRAN90 compiler

It is recommended to compile the package with ifort. If the Intel compiler is not installed already, check this link out.

BLAS/LAPACK libraries

Intel MKL

Or equivalently

BLAS
LAPACK

getexcited.py dependencies are listed in its README.

Set up

Download the stable release or clone the developmental version via git clone https://github.com/lanl/nexmd.git.
Go to the root directory of the repo. For the stable version, unzip the compressed file first. If cloning, ensure you have checked out the desired branch with git checkout <branch name>
Run make, which compiles the code with the compiler and libraries specified by options in the command line. These options can be checked and modified by editing the Makefile. Custom paths to libraries can be added to line 22 of the Makefile for all options; for further customization of other compilation flags and compilers, it is advisable to fill out the option labeled custom at line xxx. The default target is ic_mkl; running make is equivalent to make ic_mkl, which will compile NEXMD with the ifort compiler and mkl BLAS/LAPack libraries in their default location.
Optional: Add the resulting executable (default name nexmd.exe) from to your PATH. A quick way to do so in the root directory of the repo would be export PATH="$PWD:$PATH"

Tests

Example input files and their expected output are in ./tests, more information on the tests can be found here. Users are encouraged to verify the executable runs correctly by comparing the output of their executable with the expected outputs provided.

Run

It is helpful to allow nexmd.exe to access all of the available stack:

ulimit -s unlimited

If the default input filename input.ceon is used, go to the directory contains the input file and run

nexmd.exe > [output file]

Alternatively, you can run the program with an arbitrary input filename with

nexmd.exe <[input file] > [output file]

getexcited.py is typically used to call multiple nexmd.exe executions in parallel. More information on nexmd.exe can be found in the manual, more information on getexcited.py can be found in its repo.

Bug reporting

If you find a bug in the code, feel free to open a new issue or send an email to nexmd-users@lanl.gov.

Architecture

The program has several modules/sections which are based on the SQM, Amber, and CEO packages.

qmmm
davidson
others

Authors

Walter Malone, Victor M. Freixas, Xinyang Li, Hassiel Negrin-Yuvero, Royle Pérez-Castillo, Dmitry V. Makhov, Dmitrii V. Shalashilin, Nikita Fedik, Maksim Kulichenko, Richard Messerly, Luke Nambi Mohanam, Sahar Sharifzadeh, Adolfo Bastida, Shaul Mukamel, Benjamin Nebgen, Alexander White, Yu Zhang, Huajing Song, Josiah Bjorgaard, Andrew Sifain, Beatriz Rodriguez-Hernandez, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Tammie Nelson, Sergei Tretiak

Acknowledgments

Los Alamos National Lab (LANL), Center for Nonlinear Studies (CNLS), Center for Integrated Nanotechnologies (CINT)
CONICET
UNQ
ANPCyT

Copyright Notice

© 2020. Triad National Security, LLC. All rights reserved. This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration. All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so. Triad National Security, LLC as management and operations contractor for Los Alamos National Laboratory, plans to release the NexMD Software under an open source license at https://github.com/lanl/NEXMD. This software was co-authored with several individuals that include Sebastian Fernandez Alberti as professor at Universidad Nacional de Quilmes (UNQ) and Adrian Roitberg as professor at the University of Florida (UF). Triad acknowledges UNQ and UF’s role in co-authorship of the software.

License

This program is open source under the BSD-3 License. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

lanl / NEXMD