adsorption-energy

name	adsorption-energy
description	Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.

Adsorption Energy Calculation

Theory

E_ads = E(slab+adsorbate) - E(slab) - E(adsorbate_gas)

• E_ads < 0: exothermic adsorption (favorable)
• E_ads > 0: endothermic (unfavorable)

With ZPE Correction

dG_ads = G(slab+adsorbate) - G(slab) - G(adsorbate_gas)

Where G includes DFT energy + ZPE - TS from Gibbs free energy calculation.

Three Required Calculations

System	Description	Notes
slab+adsorbate	Adsorbate on surface	geo_opt with fixed bottom layers
clean slab	Same slab without adsorbate	geo_opt with same settings
adsorbate gas	Isolated molecule in box	geo_opt in large vacuum box (15+ A)

All three MUST use identical computational settings (ENCUT, EDIFF, k-points for slab systems; Gamma-only for gas molecule).

MCP Workflow

Step 1: Create workflow

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "create", "name": "CO adsorption on Pt(111)"
}}

Step 2: Build and optimize clean slab

{"tool": "catgo_fetch", "arguments": {
  "action": "crystal", "formula": "Pt", "source": "mp"
}}

{"tool": "catgo_structure", "arguments": {
  "action": "slab", "miller_index": [1,1,1],
  "min_slab_size": 12.0, "min_vacuum_size": 15.0
}}

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "add_task", "workflow_id": "wf_ads",
  "task_type": "geo_opt",
  "params": {"software": "vasp", "ENCUT": 520, "system_name": "clean_slab"}
}}

Step 3: Build and optimize slab + adsorbate

{"tool": "catgo_structure", "arguments": {
  "action": "add_atom", "element": "C", "position": [2.77, 1.60, 14.0]
}}

{"tool": "catgo_structure", "arguments": {
  "action": "add_atom", "element": "O", "position": [2.77, 1.60, 15.16]
}}

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "add_task", "workflow_id": "wf_ads",
  "task_type": "geo_opt",
  "params": {"software": "vasp", "ENCUT": 520, "system_name": "slab+CO"}
}}

Step 4: Gas-phase adsorbate

{"tool": "catgo_fetch", "arguments": {
  "action": "molecule", "name": "carbon monoxide"
}}

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "add_task", "workflow_id": "wf_ads",
  "task_type": "geo_opt",
  "params": {"software": "vasp", "ENCUT": 520, "ISMEAR": 0,
             "KPOINTS": [1,1,1], "system_name": "CO_gas"}
}}

Step 5: Submit

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "submit", "workflow_id": "wf_ads"
}}

Python API

from catgo.workflow import Workflow

wf = Workflow("CO adsorption on Pt(111)")

# Clean slab
slab_inp = wf.add_task("structure_input", structure=clean_slab_json)
slab_opt = wf.add_task("geo_opt", structure=slab_inp.output.structure,
                        software="vasp", ENCUT=520)

# Slab + CO
ads_inp = wf.add_task("structure_input", structure=slab_co_json)
ads_opt = wf.add_task("geo_opt", structure=ads_inp.output.structure,
                       software="vasp", ENCUT=520)

# Gas-phase CO (Gamma-only, no smearing)
co_inp = wf.add_task("structure_input", structure=co_gas_json)
co_opt = wf.add_task("geo_opt", structure=co_inp.output.structure,
                      software="vasp", ENCUT=520, ISMEAR=0,
                      KPOINTS=[1, 1, 1])

wf.submit()

# After completion:
# E_ads = ads_opt.output.energy - slab_opt.output.energy - co_opt.output.energy

With ZPE Correction

# Add freq + gibbs for each branch
for task_opt, name, phase in [
    (ads_opt, "slab+CO", "adsorbed"),
    (co_opt, "CO_gas", "gas"),
]:
    frq = wf.add_task("freq", structure=task_opt.output.structure,
                      software="vasp",
                      freeze_mode="layers" if phase == "adsorbed" else "none",
                      freeze_layers=4 if phase == "adsorbed" else 0)
    gib = wf.add_task("gibbs_energy", energy=task_opt.output.energy,
                      frequencies=frq.output.frequencies, phase=phase)

DAG Structure

clean_slab     --> geo_opt  ----\
slab+adsorbate --> geo_opt  ----+--> E_ads = E2 - E1 - E3
adsorbate_gas  --> geo_opt  ----/

Three independent branches, minimum 3 tasks.

Comparing Multiple Sites

To compare adsorption at different sites (top, bridge, hollow):

sites = {
    "top":    [2.77, 1.60, 14.0],
    "bridge": [1.39, 2.40, 13.8],
    "hollow": [1.39, 0.80, 13.6],
}

for site_name, pos in sites.items():
    inp = wf.add_task("structure_input", structure=make_ads_slab(pos))
    opt = wf.add_task("geo_opt", structure=inp.output.structure,
                      software="vasp", ENCUT=520,
                      system_name=f"CO_{site_name}")

Common Pitfalls

1. The gas-phase molecule must be in a large box (15+ A vacuum on all sides) with Gamma-only k-points and Gaussian smearing (ISMEAR=0).
2. For dissociative adsorption (e.g., O2 --> 2 *O), use the appropriate reference: 0.5 * E(O2_gas), not E(O_atom).
3. BSSE (basis set superposition error) is usually negligible for planewave DFT but can matter for localized basis sets (CP2K GTH).
4. If comparing different adsorbates, always use the SAME clean slab calculation as reference -- do not re-optimize the clean slab for each.
5. Check that the adsorbate did not desorb or migrate to a different site during geo_opt by inspecting the final structure.