gibbs-free-energy

name	gibbs-free-energy
description	Use when the user asks for Gibbs free energy, zero-point energy (ZPE), thermal corrections, or thermodynamic properties from DFT + frequency data.

Gibbs Free Energy Calculation

Theory

G = E_DFT + ZPE - TS

Where:

• E_DFT = electronic energy from geometry optimization (eV)
• ZPE = zero-point energy = (1/2) * sum(h * nu_i) for all real frequencies
• TS = entropic contribution at temperature T

Phase Modes

Phase	Treatment	When to Use
adsorbed	Harmonic approximation: all 3N modes treated as vibrations. No translational/rotational entropy.	Adsorbate on surface slab
gas	Ideal gas: translational + rotational + vibrational partition functions (Shomate/statistical mechanics).	Free molecule in gas phase (H2, H2O, O2, etc.)

Frequency Cutoff

Low-frequency modes (< 50 cm-1) in adsorbed species are often numerical noise from frustrated translations/rotations. These are replaced with freq_cutoff (default 50 cm-1) to avoid divergent entropy contributions.

Discussion Checkpoints

🔴 Must discuss with user:

• Phase (adsorbed vs gas) — wrong phase gives wrong entropy; adsorbed species use harmonic approximation (no translational/rotational entropy), gas-phase species use ideal gas partition function; the difference is 0.3-0.6 eV for molecules like H2O

🟡 Recommend confirming:

• Temperature (default: 298.15 K) — change for high-temperature catalysis (e.g., 600 K for thermal CO2 reduction, 373 K for steam reforming)
• Frequency cutoff (default: 50 cm-1) — replaces frustrated translations/rotations below this threshold for adsorbed species; increase to 100 cm-1 if anomalous entropy values appear

🟢 Safe defaults:

• Harmonic approximation for adsorbed species
• Ideal gas partition function for gas-phase molecules
• Pressure = 101325 Pa (1 atm)
• freq_cutoff = 50 cm-1

MCP Workflow

Step 1: Create workflow and add structure

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "create", "name": "Gibbs energy - OH on Pt(111)"
}}

Step 2: Add geo_opt task

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "add_task",
  "workflow_id": "wf_abc123",
  "task_type": "geo_opt",
  "params": {"software": "vasp", "ENCUT": 520, "EDIFFG": -0.02}
}}

Step 3: Add frequency task

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "add_task",
  "workflow_id": "wf_abc123",
  "task_type": "freq",
  "depends_on": "task_opt",
  "params": {
    "software": "vasp",
    "freeze_mode": "layers",
    "freeze_layers": 4
  }
}}

Step 4: Add gibbs_energy task

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "add_task",
  "workflow_id": "wf_abc123",
  "task_type": "gibbs_energy",
  "depends_on": ["task_opt", "task_freq"],
  "params": {
    "phase": "adsorbed",
    "temperature": 298.15,
    "freq_cutoff": 50
  }
}}

Step 5: Submit

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "submit", "workflow_id": "wf_abc123"
}}

Python API

from catgo.workflow import Workflow

wf = Workflow("Gibbs energy - OH on Pt(111)")

inp = wf.add_task("structure_input", structure=slab_oh_json)

opt = wf.add_task("geo_opt",
    structure=inp.output.structure,
    software="vasp", ENCUT=520, EDIFFG=-0.02)

frq = wf.add_task("freq",
    structure=opt.output.structure,
    software="vasp",
    freeze_mode="layers", freeze_layers=4)

gib = wf.add_task("gibbs_energy",
    energy=opt.output.energy,
    frequencies=frq.output.frequencies,
    phase="adsorbed",
    temperature=298.15,
    freq_cutoff=50)

wf.submit()

Output References

gib.output.gibbs        # G in eV
gib.output.zpe          # ZPE in eV
gib.output.entropy      # TS in eV
gib.output.enthalpy     # H in eV

Checking Results

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "get_result", "workflow_id": "wf_abc123", "task_id": "task_gibbs"
}}

Key Parameters

Parameter	Default	Description
phase	"adsorbed"	"adsorbed" (harmonic) or "gas" (ideal gas)
temperature	298.15	Temperature in Kelvin
freq_cutoff	50	Replace frequencies below this (cm-1) with this value. Adsorbed phase only.
pressure	101325	Pressure in Pa. Gas phase only.

Why Gibbs Free Energy Matters

For reaction energy diagrams (OER, HER, CO2RR, NRR), you must use Gibbs free energies, not raw DFT electronic energies. The difference matters:

Contribution	Typical magnitude
ZPE (zero-point energy)	+0.05 to +0.5 eV
-TS (entropic correction)	-0.1 to -0.6 eV
Total correction (G - E_DFT)	-0.1 to +0.3 eV

Gas-phase molecules (H2, H2O, CO2, N2) have large translational and rotational entropy contributions. Adsorbed species lose these degrees of freedom, so the correction differs significantly between gas and adsorbed phases. Omitting the gibbs_energy step introduces systematic errors of 0.2-0.5 eV per reaction step.

Every species in a reaction (intermediates AND gas-phase references) must go through: geo_opt --> freq --> gibbs_energy.

Common Pitfalls

1. Never skip the freq task -- ZPE and TS require vibrational frequencies.
2. For adsorbed species, always freeze slab bottom layers in freq calculation.
3. Gas-phase references (H2, H2O, CO2, N2, NH3) must use phase="gas" to include translational and rotational entropy.
4. The energy input must come from geo_opt (relaxed), not single_point.
5. If you get anomalously large entropy, check for near-zero frequencies -- increase freq_cutoff or verify the structure is properly relaxed.
6. Never use raw DFT energies (E_DFT) in reaction energy diagrams. Always complete the full chain: geo_opt --> freq --> gibbs_energy.