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Optimization (OPT)

Overview

OPT jobs perform local geometry optimization on the final structures from completed AIMD trajectories. Each AIMD endpoint can serve as the starting geometry for a TeraChem optimization, allowing for refinement to a local minimum or transition-state candidate structure.

Setup Instructions

1. Directory Preparation

  1. Navigate to your molecule’s working directory and ensure the following structure exists:
.../<molecule>/AIMD/
AIMD/
├── AIMS/                     # contains AIMD results (0000/, 0001/, ...)
├── AIMD_prep/                # holds shared input templates
│   ├── opt1_gen_list.sh      # generate geometry list for optimization
│   ├── opt2_execute.sh       # submit optimization jobs
│   ├── s_opt_spawn_check.sh  # monitor optimization and restart progress
│   ├── s_summarize_OPT.sh    # summarize optimization job status
│   ├── r_create_restart_opt.sh   # create restart directories (r1/, r2/, ...)
│   └── r_run_restart_opt.sh      # submit all pending restart jobs

2. AIMD_prep Setup

Within AIMD_prep/, include the following:

File Purpose
opt.in TeraChem input file for geometry optimization.
submit_opt.sh SLURM submission script for optimization jobs (edit for your cluster).

The same input and submission script are shared across all OPT jobs.

3. Core OPT Scripts

Script Description
opt1_gen_list.sh Searches AIMD directories for completed md.out files and extracts final geometries for optimization.
opt2_execute.sh Creates OPT/ directories for each geometry in opt_ready_list.txt and submits optimization jobs using submit_opt.sh.
s_opt_spawn_check.sh Scans OPT/ and OPT/r# directories for success, error, or running states; logs results.
s_summarize_OPT.sh Summarizes completed, errored, and running optimizations (including restarts).
r_create_restart_opt.sh Creates restart directories (r1/, r2/, …) for failed optimizations.
r_run_restart_opt.sh Finds and submits all pending restart jobs.

Typical Workflow

Run these scripts in sequence:

bash opt1_gen_list.sh
bash opt2_execute.sh
bash s_opt_spawn_check.sh
bash r_create_restart_opt.sh
bash r_run_restart_opt.sh
bash s_summarize_OPT.sh

4. Monitoring OPT Runs

Each optimization directory (AIMS/####/AIMD/#/OPT/) contains:

  • opt.in, coords.xyz, and opt.out
  • optional restart directories (r1/, r2/, …)

Job status is determined as follows:

Status Criteria
done opt.out contains both Job finished and Total processing time.
running Files in the directory were modified within the last few minutes.
error opt.out contains DL-FIND or HDLC errors (HDLC-errflag, Residue conversion error, DL-FIND ERROR:) or is stale.

All findings are logged to:

info_opt_spawn_check.txt
error_paths_opt_base.txt
error_paths_opt_restart.txt

5. Restart Logic

If an optimization fails:

  • r_create_restart_opt.sh extracts the final coordinates from the last valid structure in opt.out.
  • A new restart folder (r1/, r2/, …) is created inside the same OPT/ directory.
  • Each restart inherits opt.in and coords.xyz.
  • Use r_run_restart_opt.sh to automatically submit all pending restarts using the shared submit_opt.sh from AIMD_prep/.

6. Notes

  • The submit_opt.sh file is not copied into each individual OPT directory — it is referenced globally from AIMD_prep/.
  • Error markers are detected based on DL-FIND or HDLC convergence failures.
  • All scripts are restart-safe and may be rerun without duplicating submissions.
  • Ensure all scripts are executable before use:

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