{"id":20303340,"url":"https://github.com/vbhvsingh0/nxdynamics-utilities","last_synced_at":"2025-06-24T13:37:07.848Z","repository":{"id":247439076,"uuid":"825851091","full_name":"vbhvsingh0/NXdynamics-utilities","owner":"vbhvsingh0","description":"Contain sets of codes to analyze Trajectory Surface Hopping dynamics data produced through Newton-X","archived":false,"fork":false,"pushed_at":"2024-07-08T16:56:44.000Z","size":9,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-04T06:45:20.216Z","etag":null,"topics":["python","shell-scripting"],"latest_commit_sha":null,"homepage":"","language":"Python","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/vbhvsingh0.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2024-07-08T16:12:52.000Z","updated_at":"2024-07-10T15:33:17.000Z","dependencies_parsed_at":"2024-07-09T17:23:35.166Z","dependency_job_id":null,"html_url":"https://github.com/vbhvsingh0/NXdynamics-utilities","commit_stats":null,"previous_names":["vbhvsingh0/nxdynamics-utilities"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/vbhvsingh0/NXdynamics-utilities","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vbhvsingh0%2FNXdynamics-utilities","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vbhvsingh0%2FNXdynamics-utilities/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vbhvsingh0%2FNXdynamics-utilities/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vbhvsingh0%2FNXdynamics-utilities/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vbhvsingh0","download_url":"https://codeload.github.com/vbhvsingh0/NXdynamics-utilities/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vbhvsingh0%2FNXdynamics-utilities/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261686432,"owners_count":23194287,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["python","shell-scripting"],"created_at":"2024-11-14T16:36:49.789Z","updated_at":"2025-06-24T13:37:07.823Z","avatar_url":"https://github.com/vbhvsingh0.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NXdynamics-utilities\nContain sets of codes to analyze Trajectory Surface Hopping dynamics data reproduced with Newton-X.\n\nThe details about each code are provided below:\n\nPython Scripts\n\n1) collectblsandangles.py : This Python code convert XYZ coordinates of formaldehyde geometries at each time-step to the internal-coordinates(i.e. bond lengths, bond angles, and dihedrals). The code needs 'dyn.xyz' produced with Newton-X containing the geometries at each time-step. 'intcoors.txt' file is generated after successful execution of the code. Note- Play with the code ( a\u003e change number of lines to be read = number of atoms of your molecule or b\u003e Or just read the geometries of the atoms of interest) if wanting to implement this to your molecule. \n\n\nSHELL Scripts\n\n1) copyfile.sh : A simple shell script to copy a file into each TRAJn folder inside TRAJECTORIES. Note - Replace 'cp' command with 'rm' command accordingly in order to remove files recursively.\n\n2) copynxslurm.sh : A more sophisticated version of the above code. It copies the slurm file into each TRAJn folder and then replaces the digit 906 with the TRAJ number. (Useful on HPCs)\n\n3) createdynxyz.sh : This shell script creates 'dyn.xyz' from dyn.out file inside TRAJn/RESULTS'.\n\n4) runjob.sh : This script submits the job inside each TRAJn folder. (useful on HPCs)\n\n5) finalstep.sh : Useful if wanting to check the final status of all the TRAJn at the same time.\n\n6) printcharges.sh : Useful if wanting to print charges in one file at the last time step of the dynamics.\n\n7) nxslurm.sh : The slurm file to run dynamics on EXPANSE (HPC).","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvbhvsingh0%2Fnxdynamics-utilities","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvbhvsingh0%2Fnxdynamics-utilities","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvbhvsingh0%2Fnxdynamics-utilities/lists"}