⚙️ Basic Settings

Only for random configuration mode

🌡️ Quenching Parameters

Linear Quenching (Ti, ΔT, steps)

T(n+1) = T(n) - ΔT

Geometric Quenching (Ti, factor%, steps)

T(n+1) = T(n) × (1 - factor/100)

🎲 Monte Carlo Settings

🔬 Quantum Chemistry Settings

CPUs per QM calculation

Parallel evaluations

1=singlet, 2=doublet, 3=triplet

📐 Molecular Structure

Format: Element X Y Z (one atom per line)

Enter SMILES or IUPAC name to generate 3D coordinates automatically.

Examples: O (water), CCO (ethanol), C(=O)O (formic acid), C[C@@H](C(=O)O)N (alanine)

Added Molecules (nmo = 0)

No molecules added yet

📋 Protocol Builder (Optional)

Define a workflow. Leave empty for annealing-only runs.

Protocol Flags (applied to all relevant stages)

For calc/opt stages:
--retry=
--redo=
--critical= %
--skipped= %
For similarity stages:
--th=
--rmsd=
-j
Include launcher script:
../launcher.sh

📄 Input File Preview

# Add molecules and set parameters to generate preview

📦 Simulation Box Preview

Box with dummy atoms at vertices (magenta). All molecules centered at origin.

📖 Quick Reference

Protocol Stage Types:

  • rN: Run N replica annealings (default N=3)
    --box10
  • calc: Preoptimization or Single-point calculations
    /input.inp (advanced: --retry=50 --redo=3 --critical=0)
  • similarity: Cluster similar structures
    --th=2 (optional: --rmsd=2 -j4)
  • opt: Geometry optimization
    /input.inp (advanced: --retry=50 --redo=3 --skipped=0)

Common Flags:

  • --box10 - Use box with 10% effective packing
  • --retry=N - Retry failed calcs N times (default: 50)
  • --redo=N - Redo N structures (default: 3)
  • --critical=N - Max N% critical structures (mutually exclusive with --skipped)
  • --skipped=N - Max N% skipped structures (mutually exclusive with --critical)
  • --th=N - Energy similarity threshold (default: 2)
  • --rmsd=N - RMSD similarity threshold (optional)
  • -jN - Number of parallel parsing processes (optional)