VASP Frequency Calculation

Compute vibrational frequencies using finite differences. Used for zero-point energy (ZPE), thermodynamic corrections, and checking transition states.

When to Use

1. After geometry optimization — compute ZPE and Gibbs energy corrections
2. Transition state verification — confirm exactly one imaginary frequency
3. IR/Raman spectra — predict vibrational spectra
4. Thermodynamic properties — feed into gibbs_energy task

Discussion Checkpoints

🔴 Must discuss with user:

• freeze_mode — which atoms vibrate determines the thermodynamic corrections; freezing too few atoms wastes compute, freezing the adsorbate itself gives wrong ZPE
• LREAL=.FALSE. — mandatory for frequency calculations; real-space projection introduces noise that corrupts finite-difference frequencies; this is non-negotiable

🟡 Recommend confirming:

• POTIM (default: 0.015) — displacement step size; reduce to 0.01 if numerical noise appears, increase to 0.02 for heavier atoms
• NFREE (default: 2) — central differences; increase to 4 for higher accuracy at 2x cost
• ENCUT — must match the preceding geo_opt to ensure consistent forces; mismatched ENCUT invalidates the frequency data

🟢 Safe defaults:

• IBRION = 5 (finite differences)
• NSW = 1
• EDIFF = 1E-6 (tighter than geo_opt for clean forces)

Basic Frequency Calculation

from catgo.workflow import Workflow
from catgo.workflow.builtins import geo_opt, freq, gibbs_energy

wf = Workflow("Frequency calculation")
struct = wf.add_task("structure_input", structure=optimized_json)
frq = wf.add_task(freq, structure=struct.output.structure,
                  system_name="CO_gas")
wf.submit()

MCP equivalent:

catgo_workflow_engine(action="create", params={"name": "Frequency calc"})

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "structure_input",
  "structure": "<optimized_json>"
})

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "freq",
  "software": "vasp",
  "structure": "{{t_001.output.structure}}",
  "system_name": "CO_gas"
})

catgo_workflow_engine(action="submit", params={"workflow_id": "wf_xxx"})

Frozen Atoms for Slab Systems

For adsorbates on surfaces, freeze the slab atoms and only compute frequencies for the adsorbate (and optionally top surface layer). This dramatically reduces cost.

freeze_mode Options

Mode	Description	Example
"none"	All atoms vibrate (gas-phase molecules)	Small molecules
"layers"	Freeze bottom N layers by z-coordinate	freeze_mode="layers", freeze_layers=4
"z_range"	Freeze atoms below a z threshold	freeze_mode="z_range", freeze_z_below=8.0
"element"	Freeze specific elements	freeze_mode="element", freeze_elements=["Ru", "O"]
"indices"	Freeze specific atom indices	freeze_mode="indices", freeze_indices=[0,1,2,3]
"manual"	Use selective_dynamics from structure	Pre-set in POSCAR

Recommended: Freeze by Layers

For a typical slab with adsorbate:

opt = wf.add_task(geo_opt, structure=slab_oh_json,
                  ISIF=2, freeze_layers=2, system_name="*OH")

frq = wf.add_task(freq, structure=opt.output.structure,
                  freeze_mode="layers",
                  freeze_layers=4,    # Freeze bottom 4 layers (all slab atoms)
                  system_name="*OH")

Why freeze_layers=4 for freq but freeze_layers=2 for geo_opt?

• geo_opt: freeze bottom half, let top surface layers relax with adsorbate
• freq: freeze ALL slab atoms, only vibrate the adsorbate + binding site atoms
• This is physically correct: slab phonons are not relevant for adsorption thermodynamics

Freeze by Z-range

Useful when layer detection is ambiguous:

frq = wf.add_task(freq, structure=opt.output.structure,
                  freeze_mode="z_range",
                  freeze_z_below=12.5,   # Angstrom
                  system_name="*OH")

Chain: Optimization then Frequency then Gibbs Energy

The standard thermodynamics workflow:

wf = Workflow("OH adsorption Gibbs energy")
struct = wf.add_task("structure_input", structure=slab_oh_json)

# Step 1: Optimize geometry
opt = wf.add_task(geo_opt, structure=struct.output.structure,
                  ISIF=2, freeze_layers=2, system_name="*OH")

# Step 2: Frequency on optimized structure
frq = wf.add_task(freq, structure=opt.output.structure,
                  freeze_mode="layers", freeze_layers=4,
                  system_name="*OH")

# Step 3: Gibbs energy from DFT energy + frequencies
gib = wf.add_task(gibbs_energy,
                  energy=opt.output.energy,
                  frequencies=frq.output.frequencies,
                  phase="adsorbed",       # Harmonic approximation for adsorbates
                  temperature=298.15,     # K
                  freq_cutoff=50,         # cm-1, replace low freqs with this value
                  system_name="*OH")

wf.submit()

Gas-Phase Molecule Frequencies

For free molecules (H2, H2O, CO, etc.), do NOT freeze any atoms:

frq = wf.add_task(freq, structure=molecule_json,
                  freeze_mode="none",    # All atoms vibrate
                  system_name="H2O_gas")

gib = wf.add_task(gibbs_energy,
                  energy=opt.output.energy,
                  frequencies=frq.output.frequencies,
                  phase="gas",           # Ideal gas partition function
                  system_name="H2O_gas")

Gas vs adsorbed phase:

• phase="adsorbed": harmonic approximation, frustrated translations/rotations replaced by freq_cutoff
• phase="gas": ideal gas approximation with translational + rotational contributions

Key Parameters

Parameter	Default	Purpose
IBRION	5	Finite differences
NFREE	2	Central differences (2-point)
POTIM	0.015	Displacement step size (Angstrom)
EDIFF	1e-6	Tight SCF convergence (tighter than geo_opt)
LREAL	.FALSE.	Must be exact for frequencies

LREAL=.FALSE. is mandatory. Real-space projection introduces noise in forces that corrupts finite-difference frequencies. The config default overrides LREAL=Auto for freq tasks.

Analyzing Results

# Check frequencies after completion
catgo_analyze(action="frequencies", params={"task_id": "t_freq"})
# Returns: list of frequencies (cm-1), ZPE, imaginary modes

# Get raw result
catgo_workflow_engine(action="get_result", params={"task_id": "t_freq"})
# Returns: {"frequencies": [...], "zpe": 0.543}

Output

The freq task produces:

• output.frequencies — list of vibrational frequencies in cm-1 (negative = imaginary)
• output.zpe — zero-point energy in eV

Troubleshooting

Problem	Fix
Many imaginary frequencies	Structure not converged — re-optimize with tighter EDIFFG=-0.01
One imaginary frequency	Could be a transition state (expected) or shallow minimum — check mode
Frequencies seem wrong	Ensure LREAL=.FALSE. and EDIFF=1e-6
Calculation too expensive	Freeze more atoms (increase freeze_layers)
Numeric noise in frequencies	Reduce POTIM to 0.01 or increase NFREE to 4

Cost Estimate

Frequency calculations require 6N single-point calculations where N is the number of free atoms (with NFREE=2). For a 5-atom adsorbate on a frozen slab, that is 30 SCF calculations — roughly 30x the cost of a single point.