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AIMD Workflow

The AIMD workflow extends Ab Initio Multiple Spawning (AIMS) simulations by continuing nuclear motion after spawning events. It provides two interconnected components: AIMD (Molecular Dynamics) and OPT (Geometry Optimization).

Components

1. AIMD (Molecular Dynamics)

Runs trajectories on the lower electronic state, starting from geometries and velocities at AIMS spawn points. Each AIMD trajectory can evolve into multiple restart paths (r1/, r2/, …) depending on simulation success or continuation needs. These simulations allow exploration of relaxation pathways and post-spawn nuclear motion.

2. OPT (Geometry Optimization)

Performs local geometry optimizations using final structures from completed AIMD trajectories. Each AIMD endpoint becomes an input for a TeraChem optimization job, refining the structure to a minimum or transition-state candidate. Optimizations can also restart from failed runs via sequential directories (r1/, r2/, …).

Workflow Overview

  1. Run AIMS simulations to generate spawn points.

  2. Extend trajectories with AIMD using:

  3. s_summarize_AIMD.sh

  4. s_spawn_check_AIMD.sh
  5. r_create_restart_md.sh
  6. r_run_restart_md.sh
  7. Extract final AIMD geometries using opt1_gen_list.sh.

  8. Run OPT jobs using:

  9. opt2_execute.sh

  10. s_opt_spawn_check.sh
  11. r_create_restart_opt.sh
  12. r_run_restart_opt.sh

Directory Layout

<molecule>/
├── AIMS/                # completed AIMS trajectories
├── AIMD/                # AIMD workflow directory
│   ├── AIMS/            # copied or linked AIMS runs
│   ├── AIMD_prep/       # shared input templates (md.in, opt.in, submit scripts)
│   ├── s_*              # summary and monitoring scripts
│   ├── r_*              # restart creation/submission scripts
│   └── opt_*            # optimization setup and execution scripts

Current Capabilities

AIMD (Molecular Dynamics) fully implemented Optimization (OPT) integrated and operational

Notes

All scripts are designed to be modular, restart-safe, and compatible with SLURM-based HPC systems (e.g., UNC Longleaf). Ensure all scripts have execute permission before running:

chmod +x s_*.sh r_*.sh opt*.sh