surface-adsorption

name	surface-adsorption
description	Recipe for placing adsorbates on surfaces: site selection, height, orientation, periodic-image clearance.
when_to_use	Use when placing a molecule on a slab. Combine with `surface-builder` (for the slab) and `supercell-dimension-check` (for sizing).

Surface Adsorption Instructions

Common Workflow

1. Create substrate surface

   • Generate appropriate surface (see surface_creation.md)
   • Determine supercell size based on adsorbate and periodic image requirements
   • Ensure sufficient vacuum (> 10 Å, more for large adsorbates)
   • Optimize layer count for DFT cost (5 layers often sufficient)

2. Generate adsorbate molecule

   • Use ASE molecule() function for pre-optimized molecular geometries
   • Alternatively, read from database or construct manually
   • Verify molecular geometry is reasonable

3. Place adsorbate on surface

   • Choose adsorption site (top, bridge, hollow, or element-specific)
   • Set adsorption height (typical distances: 2.2-2.7 Å for O-metal bonds)
   • Orient molecule appropriately for desired adsorption mode
   • Consider multiple configurations (parallel, perpendicular orientations)

4. Verify structure integrity

   • Check all interatomic distances, especially between adsorbate and surface
   • Ensure minimum distance > 2.0 Å to avoid steric clashes
   • Calculate periodic image distances
   • Verify supercell size maintains > 10 Å between periodic images

5. Save and document

   • Save structure in appropriate format (.extxyz, POSCAR)
   • Document adsorption site, height, and orientation parameters
   • Record supercell size and layer count

Key Considerations

Supercell Sizing for Adsorbates

• Critical: Periodic images of adsorbates must be > 10 Å apart
• Calculate required supercell: account for both adsorbate size and surface unit cell
• Progressively test supercell sizes: 2x2, 3x3, 4x4, 5x5, 6x6
• Verify actual periodic image distances after construction

Supercell Sizing Examples

Surface	Supercell	Dimensions (Å)	Atoms	Use Case
SiO2 (001)	4×4×1	19.7×19.7	1152	Large adsorbates
SiO2 (100)	4×3×1	19.7×16.3	864	Medium adsorbates
SiO2 (101)	3×4×1	22.0×19.7	864	Medium adsorbates
SiO2 (110)	2×3×1	17.0×16.3	432	Small adsorbates

Layer Optimization for DFT

• Initial structures may use 8 layers for surface stability
• For DFT, reduce to 5 layers to minimize computational cost
• 5-layer structures typically reduce atoms by 40-60%
• Verify surface properties maintained with fewer layers

Adsorption Parameters

• Adsorption height: Depends on adsorbate and surface
  • O-metal: typically 2.2-2.7 Å
  • C-metal: typically 2.0-2.5 Å
  • N-metal: typically 2.0-2.5 Å
  • H-metal: typically 1.5-2.0 Å
  • Benzene on oxide: ~3.5 Å (π-stacking distance)
• Orientation: Match molecular symmetry to surface site symmetry
• Site selection: Consider coordination and reactivity

Adsorption Site Types

Site Type	Description	Typical Use
top_X	Above specific element	Element-specific binding
bridge	Between two surface atoms	Bidentate adsorption
hollow	Center of surface ring	Maximum coordination
fcc/hcp	3-fold sites on FCC	Common for close-packed

Periodic Image Distance Checking

• For each atom in adsorbate, find distance to nearest periodic image
• Minimum distance across all atoms should be > 10 Å
• Use ASE or similar tools to calculate these distances
• Larger molecules require larger supercells

Common Pitfalls and Fixes

Pitfall	Symptom	Fix
Steric clashes	Adsorbate-surface distances < 2.0 Å	Increase adsorption height; reorient molecule
Periodic image interactions	Adsorbate images < 10 Å apart	Increase supercell size (e.g., 2x2 → 3x3 or larger)
Incorrect adsorption geometry	Unexpected binding mode	Adjust molecule orientation; check adsorption site
Too large supercell	Excessive computational cost	Balance accuracy vs. cost; 10 Å is minimum threshold
Wrong surface termination	Unexpected surface chemistry	Check termination for polar surfaces

Supercell Sizing Guidelines

• 2x2 supercell: Small adsorbates only
• 3x3 supercell: May still have < 10 Å for medium adsorbates
• 4x4 supercell: Often sufficient for medium adsorbates
• 5x5 to 6x6 supercell: Required for larger molecules (e.g., benzene)
• Always verify: Calculate actual distances, don't assume

Additional Tips

Benzene Adsorption Example (SiO2)

• Benzene diameter: ~5 Å
• Recommended starting surfaces: (110) and (101) - smaller atom counts
• Site types: top_Si, top_O, bridge, hollow
• Orientations: parallel (expected most stable), perpendicular
• Adsorption height: 3.5 Å
• Recommended: parallel orientation at bridge/hollow sites

General Workflow for Adsorption Studies

1. Build bulk structure from Materials Project
2. Create multiple surface orientations
3. Optimize layer count for DFT
4. Build supercells with > 10 Å periodic image distance
5. Place adsorbate at multiple sites/orientations
6. Validate all configurations
7. Generate batch of structures for systematic study

Validation Checklist

• Minimum adsorbate-surface distance > 2.0 Å
• Periodic image distances > 10 Å
• Molecular geometry not severely distorted
• Correct surface termination
• Sufficient layers (5+ for DFT)
• Sufficient vacuum (> 10 Å)
• Documentation includes supercell size, site, orientation, height