🔍 Seam Sampling

📖 In the Seam Sampling step, NANR explores the intersection seam — the region of energetic degeneracy between two electronic states (e.g., S₀/S₁ or S₁/S₂) — using metadynamics with a seam constraint that penalizes large energy gaps.

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Concept Overview

• NANR uses RMSD-based collective variables (CVs) to drive the system along the seam.
• Periodic Gaussian bias potentials are added to discourage revisiting previous configurations.
• The seam constraint switches between linear and harmonic forms depending on the instantaneous energy gap, keeping the system near degeneracy.
• The resulting trajectory of geometries provides a map of the accessible conical intersection seam, which will later feed into clustering and MECI optimization.

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Step-By-Step Seam Sampling

1. Create a working directory

   mkdir <molecule>/seam_sampling
   

2. Add starting structure and optional orbitals

3. Place your starting geometry (e.g., FC point or MECI):

   <molecule>/seam_sampling/molecule.xyz
   

4. Optionally include orbital guesses:

   <molecule>/seam_sampling/c0
   <molecule>/seam_sampling/c0.casscf
   

5. Create seam_sampling.yaml

   filenames:
     geom_xyz: molecule.xyz             # starting xyz file
     output_dir: /<molecule>/seam_sampling
     trajectory: seam_traj.xyz          # output trajectory
   
   engine:
     type: terachem
     gpus: 0
     cwd: .
     hhtda: False
     options:
       method: rhf
       basis: 6-31gs
       precision: mixed
       scf: diis+a
       casci: 'yes'
       fon: 'yes'
       fon_temperature: 0.15
       closed: 21
       active: 4
       cassinglets: 4
       castarget: 2
       castargetmult: 1
       charge: 0
       cphfiter: 1000
       maxit: 1000
   
   dynamics:
     isc: "no"
     nsteps: 100000
     T0: 300
     gamma: 0.001
     timestep: 1.0
     constraint_theta: 0.01
     constraint_coeff: 10
     sample_fraction: 1
     sample_threshold: 0.01
     lower_state: 2
     upper_state: 3
     meta: True
     meta_tau: 25
     meta_alpha: 0.002
     meta_gamma: 1.5
     meta_maxE: 1.0
   

6. Create a submission script submit.sh

   #!/bin/bash
   #SBATCH -p l40-gpu
   #SBATCH -N 1
   #SBATCH -n 4
   #SBATCH -J seam
   #SBATCH --mem=75G
   #SBATCH -t 5-00:00:00
   #SBATCH --qos gpu_access
   #SBATCH --gres=gpu:1
   
   module load tc/25.03
   python3 /<path>/NonadiabaticNanoreactor/nanr/seam_traj.py seam_sampling.yaml
   

7. Submit your seam-sampling job

   cd <molecule>/seam_sampling
   sbatch submit.sh
   

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Outputs

• seam_traj.xyz → full metadynamics trajectory
• full_geom_seam.xyz → all collected geometries for clustering
• log/ (optional) → runtime logs and energy tracking

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Continue to 🌌 Clustering →