{"id":22668573,"url":"https://github.com/lanl/nexmd","last_synced_at":"2026-01-26T07:31:46.659Z","repository":{"id":50450008,"uuid":"276238268","full_name":"lanl/NEXMD","owner":"lanl","description":null,"archived":false,"fork":false,"pushed_at":"2024-01-31T20:06:15.000Z","size":128058,"stargazers_count":30,"open_issues_count":0,"forks_count":13,"subscribers_count":7,"default_branch":"main","last_synced_at":"2025-06-03T15:19:44.102Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Fortran","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lanl.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LicenseCopyright.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-07-01T00:27:40.000Z","updated_at":"2025-04-22T05:13:47.000Z","dependencies_parsed_at":"2024-01-28T05:20:16.054Z","dependency_job_id":"eb56a76c-dea5-4341-9747-9106a3d95a1a","html_url":"https://github.com/lanl/NEXMD","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/lanl/NEXMD","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lanl%2FNEXMD","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lanl%2FNEXMD/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lanl%2FNEXMD/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lanl%2FNEXMD/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lanl","download_url":"https://codeload.github.com/lanl/NEXMD/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lanl%2FNEXMD/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28769851,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-26T06:37:25.426Z","status":"ssl_error","status_checked_at":"2026-01-26T06:37:23.039Z","response_time":59,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-12-09T15:15:47.864Z","updated_at":"2026-01-26T07:31:46.642Z","avatar_url":"https://github.com/lanl.png","language":"Fortran","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Non-adiabatic EXcited-state Molecular Dynamics (NEXMD)\n\n`nexmd.exe` is a command-line Fortran90 program designed to understand the\nnon-radiative relaxation of a main-block molecule with 100s of atoms and 10s of\nrelevant excited states on the picosecond time scale after a vertical\nphotoexcitation. With this design goal, `nexmd.exe` has implementations of\nvarious non-adiabatic molecular dynamics(NAMD) algorithms, with efficiency and\nstability improvements to reach these time scales. To provide the electronic\nstructure parameters for these NAMD algorithms, `nexmd.exe` also performs the\nself-consistent electronic structure, linear response, quadratic response and\n'Z-vector' calculations 'on-the-fly' ; using the CEO (collective electronic\noscillator) package with semiempirical Hamiltonians from the SQM package. For\nthe classical nuclei and Tully density matrix propagation, only the classical\nnuclear geometry, nuclear velocity and the Tully density matrix at $t=0$ (when\nthe vertical excitation occurs)  need be provided. NEXMD's modular design allows\nfor individual calculations to be carried out with different control words in\nthe input file, thus NEXMD is capable of calculating, among many possibilities,\nenergy minimized geometries and absorption spectra, at the same level of theory\nas the NAMD.\n\n------\n\nNEXMD is a scientific program that assumes that the input it is given\nis worth running through its algorithms to give reproducible output.\n\n------\n\nThere is a helper Python3 script `getexcited.py` to aid in the preparation of\nthe input file, submission of a swarm of trajectories (parallelization) and\nprocessing the output (statistics and visualization), with a copy in this\nrepository.\n\n------\n\n## Highlighted Features\n\n- Solvation correction to the total energy for a single point nuclear geometry.\n- Sampling nuclear geometries of the ground-state potential energy surface (PES)\n  under NVE or NVT (through Langevin dynamics).\n- Vertical excitation stick and broadened spectrum for a single point nuclear\n  geometry or an ensemble of nuclear geometries.\n- Gaussian cube files for the transition density matrix and natural transition\n  orbitals for a vertical excitation. (Relies on external scripts as of now.)\n- Minimum energy nuclear geometry and vibrational force constants on any\n  calculated ground or excited state PES.\n- Born-Oppenheimer molecular dynamics trajectories on any calculated ground or\n  excited state PES.\n- Non-adiabatic molecular dynamics trajectories following the algorithms of\n  trajectory surface hopping (TSH), Ehrenfest, or ab-initio multiple cloning\n  (AIMC).\n- Geometry constraints for all molecular dynamics simulations. Currently\n  supports freezing bond distances or normal modes of the molecules.\n\nPlease refer to the NEXMD manual for a complete list of supported calculations.\n\n## How to cite\n\nWhen using NEXMD results in academic work, please cite the package:\n\n\u003e Walter Malone, Benjamin Nebgen, Alexander White, Yu Zhang, Huajing Song,\n\u003e Josiah A. Bjorgaard, Andrew E. Sifain, Beatriz Rodriguez-Hernandez,\n\u003e Victor M. Freixas, Sebastian Fernandez-Alberti, Adrian E. Roitberg,\n\u003e Tammie R. Nelson, and Sergei Tretiak,\n\u003e NEXMD Software Package for Nonadiabatic Excited State\n\u003e Molecular Dynamics Simulations,\n\u003e *Journal of Chemical Theory and Computation* **2020** *16* (9), 5771-5783,\n\u003e DOI: 10.1021/acs.jctc.0c00248\n\n\u003e Victor M. Freixas, Walter Malone, Xinyang Li, Huajing Song, Hassiel\n\u003e Negrin-Yuvero, Royle Pérez-Castillo, Alexander White,  Tammie R. Gibson,\n\u003e Dmitry V. Makhov, Dmitrii V. Shalashilin, Yu Zhang, Nikita Fedik, Maksim\n\u003e Kulichenko, Richard Messerly, Luke Nambi Mohanam, Sahar Sharifzadeh, Adolfo\n\u003e Bastida, Shaul Mukamel, Sebastian Fernandez-Alberti, and Sergei Tretiak, NEXMD\n\u003e v2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics\n\u003e Simulations, *Journal of Chemical Theory and Computation* **2023** *19* (16),\n\u003e 5356-5368, \u003chttps://doi.org/10.1021/acs.jctc.3c00583\u003e\n\nas well as the 2020 review of the methods implemented in NEXMD:\n\n\u003e Tammie R. Nelson, Alexander J. White, Josiah A. Bjorgaard,\n\u003e Andrew E. Sifain, Yu Zhang, Benjamin Nebgen, Sebastian Fernandez-Alberti,\n\u003e Dmitry Mozyrsky, Adrian E. Roitberg, and Sergei Tretiak,\n\u003e Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications\n\u003e for Modeling Photophysics in Extended Molecular Materials,\n\u003e *Chemical Reviews* **2020** *120* (4), 2215-2287,\n\u003e DOI: 10.1021/acs.chemrev.9b00447\n\nwe encourage users to cite the references and libraries used by\nNEXMD, which are detailed in the NEXMD manual.\n\n## Usage\n\n### Prerequisites\n\nThe following dependencies must be installed and configured before\ncompiling `nexmd.exe`: (1) a build automation tool such as `make`, (2) a\nFORTRAN90 compiler, (3) and a BLAS/LAPack library compatible with the\ncompiler and associated libraries.\n\n1. Build automation tool\n\n`make` is a standard tool\n\n2. FORTRAN90 compiler\n\n- It is recommended to compile the package with `ifort`. If the Intel compiler is\nnot installed already, check [this\nlink](https://www.intel.com/content/www/us/en/developer/tools/oneapi/fortran-compiler.html#gs.**8srmr7**)\nout.\n\n3. BLAS/LAPACK libraries\n\n- [Intel\n  MKL](https://www.intel.com/content/www/us/en/develop/documentation/get-started-with-mkl-for-dpcpp/top.html)\n\nOr equivalently\n\n- [BLAS](http://www.netlib.org/blas/)\n- [LAPACK](http://www.netlib.org/lapack)\n\n`getexcited.py` dependencies are listed in its README.\n\n### Set up\n\n- Download the [stable release](https://github.com/lanl/nexmd/releases/latest)\n  or clone the developmental version via `git clone\n  https://github.com/lanl/nexmd.git`.\n- Go to the root directory of the repo. For the stable version, unzip the\n  compressed file first. If cloning, ensure you have checked out the desired\n  branch with `git checkout \u003cbranch name\u003e`\n- Run `make`, which compiles the code with the compiler and libraries specified\n  by options in the command line. These options can be checked and modified by\n  editing the [Makefile](./Makefile). Custom paths to libraries can be added to\n  line 22 of the [Makefile](./Makefile) for all options; for further\n  customization of other compilation flags and compilers, it is advisable to\n  fill out the option labeled custom at line 415. The default target is\n  `ic_mkl`; running `make` is equivalent to `make ic_mkl`, which will compile\n  NEXMD with the `ifort` compiler and `mkl` BLAS/LAPack libraries in their\n  default location.\n  \n- **Optional:** Add the resulting executable (default name `nexmd.exe`) from\n  to your PATH. A quick way to do so in the root directory of the repo\n  would be `export PATH=\"$PWD:$PATH\"`\n\n### Tests\n\nExample input files and their expected output are in `./tests`, more information\n on the tests can be found [here](./tests/README.md). Users are encouraged to\nverify the executable runs correctly by comparing the output of their\nexecutable with the expected outputs provided.\n\n### Run\n\nIt is helpful to allow `nexmd.exe` to access all of the available stack:\n\n```shell\nulimit -s unlimited\n```\n\nIf the default input filename `input.ceon` is used, go to the directory\ncontains the input file and run\n\n```shell\nnexmd.exe \u003e [output file]\n```\n\nAlternatively, you can run the program with an arbitrary input filename with\n\n```shell\nnexmd.exe \u003c[input file] \u003e [output file]\n```\n\n`getexcited.py` is typically used to call multiple `nexmd.exe` executions in\nparallel. More information on nexmd.exe can be found in the\n[manual](./manual/documentation.pdf), more information on getexcited.py can be\nfound in its repo.\n\n## Bug reporting\n\nIf you find a bug in the code, feel free to [open a new\nissue](https://github.com/lanl/NEXMD/issues/new) or send an email to\n\u003cnexmd-users@lanl.gov\u003e.\n\n## Architecture\n\nThe program has several modules/sections which are based on the SQM, Amber, and\nCEO packages.\n\n- qmmm\n- davidson\n- others\n\n## Authors\n\nWalter Malone, Victor M. Freixas, Xinyang Li, Hassiel Negrin-Yuvero,\nRoyle Pérez-Castillo, Dmitry V. Makhov, Dmitrii V. Shalashilin,\nNikita Fedik, Maksim Kulichenko, Richard Messerly, Luke Nambi Mohanam,\nSahar Sharifzadeh, Adolfo Bastida, Shaul Mukamel, Benjamin Nebgen,\nAlexander White, Yu Zhang, Huajing Song, Josiah Bjorgaard,\nAndrew Sifain, Beatriz Rodriguez-Hernandez, Sebastian Fernandez-Alberti,\nAdrian E. Roitberg, Tammie Nelson, Sergei Tretiak\n\n## Acknowledgments\n\n- Los Alamos National Lab (LANL), Center for Nonlinear Studies (CNLS), Center\n  for Integrated Nanotechnologies (CINT)\n- CONICET\n- UNQ\n- ANPCyT\n  \n## Copyright Notice\n\n© 2020. Triad National Security, LLC. All rights reserved. This program was\nproduced under U.S. Government contract 89233218CNA000001 for Los Alamos\nNational Laboratory (LANL), which is operated by Triad National Security, LLC\nfor the U.S. Department of Energy/National Nuclear Security Administration. All\nrights in the program are reserved by Triad National Security, LLC, and the\nU.S. Department of Energy/National Nuclear Security Administration. The\nGovernment is granted for itself and others acting on its behalf a\nnonexclusive, paid-up, irrevocable worldwide license in this material to\nreproduce, prepare derivative works, distribute copies to the public, perform\npublicly and display publicly, and to permit others to do so. Triad National\nSecurity, LLC as management and operations contractor for Los Alamos National\nLaboratory, plans to release the NexMD Software under an open source license at\n\u003chttps://github.com/lanl/NEXMD\u003e. This software was co-authored with several\nindividuals that include Sebastian Fernandez Alberti as professor at\nUniversidad Nacional de Quilmes (UNQ) and Adrian Roitberg as professor at the\nUniversity of Florida (UF). Triad acknowledges UNQ and UF’s role in\nco-authorship of the software.\n\n## License\n\nThis program is open source under the BSD-3 License. Redistribution and use in\nsource and binary forms, with or without modification, are permitted provided\nthat the following conditions are met:  \n\n1. Redistributions of source code must retain the above copyright notice, this\nlist of conditions and the following disclaimer.\n1. Redistributions in binary form must reproduce the above copyright notice,\nthis list of conditions and the following disclaimer in the documentation\nand/or other materials provided with the distribution.\n1. Neither the name of the copyright holder nor the names of its contributors\nmay be used to endorse or promote products derived from this software without\nspecific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND\nANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED\nWARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flanl%2Fnexmd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flanl%2Fnexmd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flanl%2Fnexmd/lists"}