run_gsm.py

This module executes Bash script gsm.sh which exists in every GSM job and generates the corresponding outputs. This uses ProcessPoolExecutor to run the script in parallel for each gsm job directory.

  ├── 0000_string.png
  ├── grown_string_000.xyz
  ├── grown_string1_000.xyz
  ├── gsm_log
  ├── gsm.sh
  ├── IC_data_0000.txt
  ├── initial.xyz
  ├── ISOMERS.txt
  ├── lot_jobs_0.txt
  ├── lot_jobs_1.txt
  ├── lot_jobs_2.txt
  ├── lot_jobs_3.txt
  ├── lot_jobs_4.txt
  ├── lot_jobs_5.txt
  ├── lot_jobs_6.txt
  ├── lot_jobs_7.txt
  ├── lot_jobs_8.txt
  ├── opt_converged_000.xyz
  ├── scratch
  │   └── 000
  └── TSnode_0.xyz

File/Directory	Description
string.png	Diagram showing the energy for every node during the reaction.
gsm_log	Log file containing details of the GSM calculation.
IC_data.txt	File with internal coordinate data.
initial.xyz	Represents the geometry of the initial structure.
lot_jobs.txt	Lot job details containing the optimization process for each node.
opt_converged.xyz	File with optimized and converged geometry.
scratch	Directory for storing temporary files or data generated during calculations.
TSnode.xyz	Represents the geometry of the transition state node.

string.png

You can observe the process of a GSM job through the generated .png file.