Adsorbate Placement

Overview

The adsorbate_place task type places adsorbate molecules on surface slabs. It uses ferrox (Rust) find_adsorption_sites to locate surface sites, then the CatGo placement engine (utils/adsorbate_placement.py) for Rodrigues rotation, overlap detection, and multi-dentate support.

Task Type: adsorbate_place

• Type: adsorbate_place (local task, no HPC needed)
• Engine: ferrox site finder + CatGo placement engine
• Outputs: structure (slab+adsorbate as JSON)

Parameters

Parameter	Type	Default	Description
structure	JSON	required	Slab structure input
species	str	"OH"	Adsorbate species name
site	str	"ontop"	Site type: "ontop", "bridge", "hollow", or "all"
height	float	2.0	Height above surface in Angstroms
site_index	int	0	Which site of the given type to use (0 = first)

Supported Adsorbate Species

Species	Atoms	Binding Atom	Notes
OH	O, H	O	Hydroxyl, O-H = 0.96 A
O	O	O	Atomic oxygen
OOH	O, O, H	O1	Hydroperoxo, key OER intermediate
H	H	H	Atomic hydrogen
H2O	O, H, H	O	Water molecule
CO	C, O	C	Carbon monoxide, C-O = 1.13 A
CO2	C, O, O	C	Carbon dioxide, linear
N2	N, N	N	Dinitrogen, N-N = 1.10 A
NH	N, H	N	Imide
NH2	N, H, H	N	Amino
NH3	N, H, H, H	N	Ammonia
CHO	C, H, O	C	Formyl
COOH	C, O, O, H	C	Carboxyl

Site Types

Site	ferrox Type	Coordination	Description
ontop	atop	1-fold	Directly above one surface atom
bridge	bridge	2-fold	Between two surface atoms
hollow	hollow3	3-fold	Above threefold hollow site
all	atop (default)	1-fold	Auto-selects ontop

Discussion Checkpoints

🔴 Must discuss with user:

• Adsorbate species — determines the chemistry being studied; wrong species = wrong intermediate in the reaction pathway
• Adsorption site (ontop/bridge/hollow) — different sites have different binding energies; for screening, test all three and report the most stable

🟡 Recommend confirming:

• Height above surface (default: 2.0 A) — too close triggers repulsion during geo_opt, too far causes adsorbate to fly away; use 1.5-1.8 A for atomic O, 2.0-2.5 A for molecular species
• Site index (default: 0) — which specific site of the given type; call catgo_analyze(action="adsorption_sites") first to see available sites
• Multi-dentate orientation — for OOH, COOH, and other multi-atom adsorbates, the binding orientation matters; verify with catgo_view after placement

🟢 Safe defaults:

• Collision detection enabled (ferrox automatic)
• Automatic site finding via ferrox find_adsorption_sites
• Binding atom orientation follows species convention (O down for OH, C down for CO)

MCP Workflow: Place Adsorbate on Slab

Step 1: Generate slab (or use existing)

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

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

{"tool": "catgo_structure", "arguments": {
  "action": "supercell",
  "scaling": [2, 2, 1]
}}

Step 2: Find adsorption sites

{"tool": "catgo_analyze", "arguments": {
  "action": "adsorption_sites"
}}

This returns all available sites (ontop, bridge, hollow) with coordinates.

Step 3: Build workflow with adsorbate placement

Using the workflow engine with adsorbate_place node:

{"tool": "catgo_workflow", "arguments": {
  "action": "batch",
  "workflow_id": "wf_123",
  "operations": [
    {"op": "add_node", "node_type": "slab_gen", "label": "slab1",
     "params": {"miller": [1, 1, 1], "layers": 4, "vacuum": 15.0}},
    {"op": "add_node", "node_type": "adsorbate_place", "label": "ads1",
     "params": {"species": "OH", "site": "ontop", "height": 2.0, "site_index": 0}},
    {"op": "add_node", "node_type": "geo_opt", "label": "go1",
     "params": {"software": "vasp", "ENCUT": 520, "freeze_mode": "layers", "freeze_layers": 2}},
    {"op": "connect", "from_id": "<structure_input_id>", "to_id": "slab1"},
    {"op": "connect", "from_id": "slab1", "to_id": "ads1",
     "from_handle": "structure", "to_handle": "structure"},
    {"op": "connect", "from_id": "ads1", "to_id": "go1",
     "from_handle": "structure", "to_handle": "structure"}
  ]
}}

Step 4: PENDING_REVIEW -- verify adsorbate position

The user should inspect the structure before submitting geo_opt. Check:

• Adsorbate is at the correct site (ontop/bridge/hollow)
• Height above surface is reasonable (1.5-2.5 A for most species)
• No atom overlaps or unrealistic bond lengths
• Binding atom orientation is correct (e.g., C down for CO, O down for OH)

{"tool": "catgo_view", "arguments": {"action": "get_state"}}

Step 5: Submit for DFT optimization

{"tool": "catgo_workflow", "arguments": {
  "action": "run",
  "workflow_id": "wf_123",
  "run_config": {"cluster": "expanse", "partition": "shared", "walltime": "04:00:00"}
}}

Python API

from catgo.workflow import Workflow

wf = Workflow("OH on Pt(111)")

# Bulk input
inp = wf.add_task("structure_input", structure=pt_bulk_json)

# Cut slab
slab = wf.add_task("slab_gen",
    structure=inp.output.structure,
    miller=(1, 1, 1),
    layers=4,
    vacuum=15.0)

# Place adsorbate
ads = wf.add_task("adsorbate_place",
    structure=slab.output.structure,
    species="OH",
    site="ontop",
    height=2.0,
    site_index=0)

# PENDING_REVIEW: user should verify adsorbate position before geo_opt

# Geometry optimization
opt = wf.add_task("geo_opt",
    structure=ads.output.structure,
    software="vasp",
    ENCUT=520,
    freeze_mode="layers",
    freeze_layers=2)

wf.submit()

Complete OER Workflow Example

The oxygen evolution reaction (OER) has four intermediates: *OH, *O, *OOH, and clean slab. Each needs geo_opt + freq + gibbs_energy.

from catgo.workflow import Workflow

wf = Workflow("OER on IrO2(110)")

# Shared bulk input
inp = wf.add_task("structure_input", structure=iro2_bulk_json)
slab = wf.add_task("slab_gen",
    structure=inp.output.structure,
    miller=(1, 1, 0), layers=4, vacuum=15.0)

# --- Clean slab branch ---
slab_opt = wf.add_task("geo_opt", structure=slab.output.structure,
    software="vasp", ENCUT=520, system_name="clean_slab",
    freeze_mode="layers", freeze_layers=2)
slab_freq = wf.add_task("freq", structure=slab_opt.output.structure,
    software="vasp", freeze_mode="layers", freeze_layers=2)
slab_gibbs = wf.add_task("gibbs_energy",
    energy=slab_opt.output.energy,
    frequencies=slab_freq.output.frequencies,
    phase="adsorbed")

# --- *OH branch ---
oh_ads = wf.add_task("adsorbate_place", structure=slab.output.structure,
    species="OH", site="ontop", height=2.0)
oh_opt = wf.add_task("geo_opt", structure=oh_ads.output.structure,
    software="vasp", ENCUT=520, system_name="OH_ads",
    freeze_mode="layers", freeze_layers=2)
oh_freq = wf.add_task("freq", structure=oh_opt.output.structure,
    software="vasp", freeze_mode="layers", freeze_layers=2)
oh_gibbs = wf.add_task("gibbs_energy",
    energy=oh_opt.output.energy,
    frequencies=oh_freq.output.frequencies,
    phase="adsorbed")

# --- *O branch ---
o_ads = wf.add_task("adsorbate_place", structure=slab.output.structure,
    species="O", site="ontop", height=1.8)
o_opt = wf.add_task("geo_opt", structure=o_ads.output.structure,
    software="vasp", ENCUT=520, system_name="O_ads",
    freeze_mode="layers", freeze_layers=2)
o_freq = wf.add_task("freq", structure=o_opt.output.structure,
    software="vasp", freeze_mode="layers", freeze_layers=2)
o_gibbs = wf.add_task("gibbs_energy",
    energy=o_opt.output.energy,
    frequencies=o_freq.output.frequencies,
    phase="adsorbed")

# --- *OOH branch ---
ooh_ads = wf.add_task("adsorbate_place", structure=slab.output.structure,
    species="OOH", site="ontop", height=2.0)
ooh_opt = wf.add_task("geo_opt", structure=ooh_ads.output.structure,
    software="vasp", ENCUT=520, system_name="OOH_ads",
    freeze_mode="layers", freeze_layers=2)
ooh_freq = wf.add_task("freq", structure=ooh_opt.output.structure,
    software="vasp", freeze_mode="layers", freeze_layers=2)
ooh_gibbs = wf.add_task("gibbs_energy",
    energy=ooh_opt.output.energy,
    frequencies=ooh_freq.output.frequencies,
    phase="adsorbed")

# --- Gas-phase references (H2O, H2) ---
h2o_inp = wf.add_task("structure_input", structure=h2o_gas_json)
h2o_opt = wf.add_task("geo_opt", structure=h2o_inp.output.structure,
    software="vasp", ENCUT=520, ISMEAR=0, KPOINTS=[1,1,1],
    system_name="H2O_gas")
h2o_freq = wf.add_task("freq", structure=h2o_opt.output.structure,
    software="vasp")
h2o_gibbs = wf.add_task("gibbs_energy",
    energy=h2o_opt.output.energy,
    frequencies=h2o_freq.output.frequencies,
    phase="gas")

h2_inp = wf.add_task("structure_input", structure=h2_gas_json)
h2_opt = wf.add_task("geo_opt", structure=h2_inp.output.structure,
    software="vasp", ENCUT=520, ISMEAR=0, KPOINTS=[1,1,1],
    system_name="H2_gas")
h2_freq = wf.add_task("freq", structure=h2_opt.output.structure,
    software="vasp")
h2_gibbs = wf.add_task("gibbs_energy",
    energy=h2_opt.output.energy,
    frequencies=h2_freq.output.frequencies,
    phase="gas")

# Free energy diagram
fed = wf.add_task("free_energy_diagram",
    gibbs_values={
        "clean": slab_gibbs.output.gibbs,
        "OH": oh_gibbs.output.gibbs,
        "O": o_gibbs.output.gibbs,
        "OOH": ooh_gibbs.output.gibbs,
        "H2O": h2o_gibbs.output.gibbs,
        "H2": h2_gibbs.output.gibbs,
    },
    step_order=["clean", "OH", "O", "OOH", "O2"])

wf.submit()

DAG Structure (Single Adsorbate)

bulk_crystal --> slab_gen --> adsorbate_place --> [PENDING_REVIEW] --> geo_opt

DAG Structure (OER)

                                /--> *OH  --> geo_opt --> freq --> gibbs --\
bulk --> slab_gen --> slab -----+--> *O   --> geo_opt --> freq --> gibbs ---+--> free_energy_diagram
                          \    \--> *OOH --> geo_opt --> freq --> gibbs --/
                           \--> clean_slab --> geo_opt --> freq --> gibbs -/

Comparing Multiple Sites

To compare adsorption at different sites (ontop, bridge, hollow), create separate branches from the same slab:

for site_type in ["ontop", "bridge", "hollow"]:
    ads = wf.add_task("adsorbate_place",
        structure=slab.output.structure,
        species="OH",
        site=site_type,
        height=2.0,
        site_index=0)
    opt = wf.add_task("geo_opt",
        structure=ads.output.structure,
        software="vasp", ENCUT=520,
        system_name=f"OH_{site_type}")

Common Pitfalls

1. Always build the slab and supercell BEFORE placing adsorbates. Adding adsorbates to a 1x1 slab gives unphysically high coverage.
2. The initial height matters: too close triggers repulsion, too far may cause the adsorbate to fly away during geo_opt. Use 1.5-2.5 A for most species.
3. OOH tends to dissociate into O + OH during relaxation on some surfaces. Use tight EDIFFG and monitor the trajectory.
4. For bridge and hollow sites, the adsorbate is placed between atoms automatically by the ferrox site finder. Do not manually calculate midpoints.
5. After placement, always verify with catgo_view that no atoms overlap and the geometry looks reasonable before submitting to DFT.
6. When using site_index, call catgo_analyze with action: "adsorption_sites" first to see available sites and their indices.
7. The site="all" option defaults to ontop (atop) sites. For specific site types, always pass the explicit type name.