strain-deformation

name	strain-deformation
description	Use when the user asks to apply strain, deformation, lattice distortion, or mechanical loading to a periodic structure (uniaxial, biaxial, hydrostatic, or shear).
tags	["structure","strain","deformation","mechanical","elastic"]

Strain / Deformation

Overview

Applies mechanical strain to periodic structures by deforming the lattice. This is used for:

• Strain engineering: Tuning electronic structure and catalytic activity
• Elastic property calculations: Computing elastic tensors from stress-strain curves
• Phase stability: Testing structural stability under deformation
• Epitaxial strain: Modeling lattice mismatch in thin films and heterostructures

Four strain types are supported:

• Uniaxial: Stretch/compress along a single axis (a, b, or c)
• Biaxial: Stretch/compress in the ab-plane simultaneously
• Hydrostatic: Uniform expansion/compression in all three directions
• Shear: Off-diagonal deformation (tilting)

MCP Tool: catgo_structure (via REST /build/strain)

Strain is applied through the /build/strain endpoint. In the full MCP server, use the catgo_build_strain tool.

Apply Uniaxial Strain

Stretch a structure by 2% along the c-axis:

POST /build/strain
{
  "structure": { ... },
  "strain_type": "uniaxial",
  "axis": "c",
  "magnitude": 0.02,
  "n_steps": 1
}

Apply Biaxial Strain

Stretch in the ab-plane (common for surface/thin-film studies):

POST /build/strain
{
  "structure": { ... },
  "strain_type": "biaxial",
  "magnitude": 0.03,
  "n_steps": 1
}

Apply Hydrostatic Strain

Uniform expansion by 1%:

POST /build/strain
{
  "structure": { ... },
  "strain_type": "hydrostatic",
  "magnitude": 0.01,
  "n_steps": 1
}

Apply Shear Strain

Off-diagonal deformation:

POST /build/strain
{
  "structure": { ... },
  "strain_type": "shear",
  "magnitude": 0.02,
  "n_steps": 1
}

Generate Multiple Strain Steps

Generate a series of strained structures (e.g., for elastic constant calculations). Setting n_steps > 1 creates structures at evenly spaced magnitudes from -|magnitude| to +|magnitude|:

POST /build/strain
{
  "structure": { ... },
  "strain_type": "uniaxial",
  "axis": "c",
  "magnitude": 0.05,
  "n_steps": 11
}

This returns 11 structures at -5%, -4%, ..., 0%, ..., +4%, +5% strain.

Parameters

Parameter	Type	Default	Description
strain_type	string	"uniaxial"	Type: uniaxial, biaxial, hydrostatic, shear
axis	string	"c"	Axis for uniaxial strain: a, b, or c
magnitude	float	0.02	Strain magnitude (fraction, e.g., 0.02 = 2%)
n_steps	int	1	Number of strain steps (1 = single deformation)
structure	dict	--	Structure in pymatgen dict format

Complete Workflow: Elastic Constants via Stress-Strain

1. Fetch and relax structure

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

{"tool": "catgo_workflow", "arguments": {
  "action": "create", "name": "Cu elastic constants"
}}

{"tool": "catgo_workflow", "arguments": {
  "action": "add_node", "workflow_id": "wf_elastic",
  "node_type": "cell_opt",
  "params": {"software": "vasp", "ENCUT": 520,
             "system_name": "Cu cell opt"}
}}

2. Apply strain series and compute stresses

For each deformation mode (6 independent strains for cubic symmetry), apply a series of strains and run single-point calculations to get stress tensors.

3. Fit elastic tensor

Use the workflow elastic_analysis node to fit the elastic tensor from the stress-strain data:

{"tool": "catgo_workflow", "arguments": {
  "action": "add_node", "workflow_id": "wf_elastic",
  "node_type": "elastic_analysis",
  "params": {"sym_reduce": true, "n_strains": 6, "strain_magnitude": 0.02}
}}

Deformation Matrix Reference

Strain Type	Deformation Matrix
Uniaxial (c)	diag(1, 1, 1+e)
Biaxial (ab)	diag(1+e, 1+e, 1)
Hydrostatic	diag(1+e, 1+e, 1+e)
Shear	[[1, e, 0], [0, 1, 0], [0, 0, 1]]

Where e is the strain magnitude.

Common Pitfalls

1. Strain magnitudes are fractional (0.02 = 2%). Typical values for elastic property calculations are 0.5-5%.
2. Always relax the original structure first (cell_opt) before applying strain. Straining an unrelaxed structure gives meaningless results.
3. For strain-activity relationships in catalysis, apply strain to the slab (not the bulk) and re-optimize adsorbate positions. The strained slab should have fixed lattice vectors during geo_opt (ISIF=2).
4. When using n_steps > 1, structures are generated symmetrically around zero strain. This is important for elastic constant fitting (need both tensile and compressive data).
5. Shear strain breaks symmetry. For elastic constant calculations, use the full set of 6 independent deformations for the relevant crystal system.