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Molecular Dynamics (AIMD)

Overview

AIMD (Ab Initio Molecular Dynamics) continues nuclear motion after AIMS spawning events. Each spawn point from an AIMS trajectory is extended into a physically meaningful MD trajectory on the lower electronic state, allowing exploration of post-spawn dynamics.

Setup Instructions

1. Directory Preparation

  1. Navigate to your molecule’s AIMS working directory:

bash .../<molecule>/AIMS/#### 2. Create a top-level AIMD directory:

bash .../<molecule>/AIMD/ 3. Inside it, copy or link the finished AIMS run directories (e.g., 0000/, 0001/, 0002/) into:

bash .../<molecule>/AIMD/AIMS/

Each of these AIMS trajectories will serve as a starting point for MD spawning.

2. AIMD_prep Setup

Create a preparation folder:

.../<molecule>/AIMD/AIMD_prep/

Inside AIMD_prep/, include the following:

File Purpose
md.in TeraChem input file for AIMD dynamics.
submit_md.sh SLURM submission script for AIMD jobs (edit to match your cluster queue).

These serve as shared templates for all AIMD trajectories and restarts.

3. Core AIMD Scripts

Place these scripts in your main AIMD working directory (e.g., .../<molecule>/AIMD_TEST/):

Script Description
s_summarize_AIMD.sh Summarizes how many AIMD spawns are finished, running, or errored.
s_spawn_check_AIMD.sh Scans all AIMD and restart (r#) directories for success, error, or active jobs.
r_create_restart_md.sh Generates restart directories (r1/, r2/, …) for failed trajectories.
r_run_restart_md.sh Finds and submits all pending restart jobs automatically.

Typical Workflow

Run the following in sequence:

bash s_summarize_AIMD.sh
bash s_spawn_check_AIMD.sh
bash r_create_restart_md.sh
bash r_run_restart_md.sh

4. Monitoring AIMD Runs

Each trajectory folder (AIMS/####/AIMD/#/) contains:

  • md.in, coords.xyz, vels.xyz, and md.out
  • optional restart directories (r1/, r2/, etc.)

Job status is determined as follows:

Status Criteria
done md.out contains both | Job finished:and| Total processing time:
running Files in the directory were modified within the last few minutes.
error md.out contains termination keywords (e.g., DIE called at, Job terminated) or is stale.

All findings are logged to:

info_spawn_check_AIMD.txt
error_paths_base.txt
error_paths_restart.txt

5. Restart Logic

If a trajectory fails:

  • r_create_restart_md.sh extracts the final coordinates and velocities from the last valid frame.
  • A new restart folder (r1/, r2/, …) is created within the corresponding AIMD spawn.
  • Each restart inherits md.in, coords.xyz, and vels.xyz.
  • Use r_run_restart_md.sh to automatically submit all pending restart jobs.

6. Notes

  • Copying many AIMS runs to AIMD can be slow — use a batch copy script (e.g., aimd_aims_copy.sh) and submit it through SLURM instead of running locally.
  • All scripts are restart-safe: repeated executions skip completed or active runs.
  • Ensure all scripts are executable before running:
chmod +x s_*.sh r_*.sh