energy-diagram

name	energy-diagram
description	Use when the user asks to generate a reaction energy diagram, free energy profile, potential energy surface plot, or pathway comparison diagram for catalysis or reaction mechanism studies.
tags	["analysis","catalysis","energy-diagram","free-energy","pathway","Plotly"]

Energy Diagram Generation

Overview

Generates Plotly-compatible reaction energy pathway diagrams from computed intermediate and transition-state energies. The output includes horizontal line segments for intermediates, cubic-spline curves for transition states, and dashed connectors between consecutive steps.

Key applications:

• Reaction mechanism comparison: Overlay multiple pathways on one diagram
• Catalysis studies: Visualize OER, HER, CO2RR, NRR free energy profiles
• Transition state analysis: Show activation barriers as TS arches
• Publication figures: Export as SVG/PNG from the Plotly viewer

MCP Tool: catgo_catalysis_energy_diagram

In the full MCP server, use the catgo_catalysis_energy_diagram tool. In the workflow engine, the free_energy node generates energy diagrams automatically from upstream gibbs_energy nodes.

Generate a Simple Energy Diagram

{"tool": "catgo_catalysis_energy_diagram", "arguments": {
  "pathways": [
    {
      "name": "OER on RuO2(110)",
      "color": "#1f77b4",
      "steps": [
        {"label": "*", "energy": 0.0},
        {"label": "*OH", "energy": 0.85},
        {"label": "*O", "energy": 1.60},
        {"label": "*OOH", "energy": 3.20},
        {"label": "O2", "energy": 4.92}
      ]
    }
  ]
}}

Compare Multiple Pathways

{"tool": "catgo_catalysis_energy_diagram", "arguments": {
  "pathways": [
    {
      "name": "RuO2(110)",
      "color": "#1f77b4",
      "steps": [
        {"label": "*", "energy": 0.0},
        {"label": "*OH", "energy": 0.85},
        {"label": "*O", "energy": 1.60},
        {"label": "*OOH", "energy" 
           
      
    
    
       
       
       
           
           
           
           
           
      
    
  

Include Transition States

Mark transition states with "is_ts": true. These appear as cubic-spline arches between the adjacent intermediates:

{"tool": "catgo_catalysis_energy_diagram", "arguments": {
  "pathways": [
    {
      "name": "CO oxidation on Pt(111)",
      "color": "#2ca02c",
      "steps": [
        {"label": "CO* + O*", "energy": 0.0},
        {"label": "TS", "energy": 0.85, "is_ts": true},
        {"label": "CO2(g)", "energy": -1.20}
      ]
    }
  

Custom Layout Configuration

{"tool": "catgo_catalysis_energy_diagram", "arguments": {
  "pathways": [ ... ],
  "config": {
    "height": 500,
    "y_label": "Gibbs Free Energy (eV)",
    "x_label": "Reaction Coordinate",
    "energy_format": ".3f",
    "line_width": 4
  }
}}

Parameters

pathways (required)

Array of pathway objects. Each pathway contains:

Field	Type	Required	Description
name	string	no	Legend label for this pathway
color	string	no	Line color (CSS color, e.g., "#1f77b4")
steps	list[dict]	yes	Ordered list of intermediates and TSs

Each step dict:

Field	Type	Required	Description
label	string	yes	State label (e.g., "*OH", "TS1")
energy	float	yes	Energy in eV
is_ts	bool	no	True for transition states (default false)

config (optional)

Parameter	Type	Default	Description
base_spacing	float	1.0	Base horizontal spacing between states
hline_ratio	float	0.3	Width of horizontal energy lines
ts_spacing_ratio	float	0.4	Width of TS spline curves
vline_ratio	float	0.3	Width of dashed connectors
line_width	float	3	Line thickness
energy_format	string	".2f"	Python format string for energy labels
height	int	450	Plot height in pixels
y_label	string	"Free Energy (eV)"	Y-axis title
x_label	string	"Reaction Coordinate"	X-axis title

Return Format

{
  "traces": [ ... ],
  "layout": { ... },
  "annotations": [ ... ]
}

The return value is directly compatible with Plotly: pass traces as the data array, merge annotations into layout.annotations, and render with Plotly.newPlot(div, traces, layout).

Workflow Integration: free_energy Node

In the CatGo workflow engine, the free_energy node automatically generates an energy diagram from upstream gibbs_energy nodes:

{"tool": "catgo_workflow", "arguments": {
  "action": "batch",
  "workflow_id": "wf_oer",
  "operations": [
    {"op": "add_node", "node_type": "free_energy", "label": "diagram",
     "params": {"input_mode": "auto"}},
    {"op": "connect", "from_id": "gibbs_oh", "to_id": "diagram",
     "from_handle": "gibbs", "to_handle" 
         
        
         
        
  

The free_energy node collects Gibbs energies from all connected upstream nodes and arranges them into a pathway diagram automatically.

Important: Use Gibbs Free Energies, NOT DFT Energies

All energy values passed to this tool must be Gibbs free energies (G), not raw DFT electronic energies (E_DFT). Each intermediate and gas-phase reference must go through the full chain: geo_opt --> freq --> gibbs_energy.

G = E_DFT + ZPE - TS

Using raw E_DFT omits zero-point energy (ZPE) and entropy (TS), which contribute 0.2-0.5 eV per intermediate. This makes the resulting diagram quantitatively wrong and can change which step is potential-determining.

For electrochemical reactions (OER, HER, CO2RR, NRR), also apply:

• Atom balancing with gas-phase references (H2, H2O, CO2, N2, NH3)
• pH correction: subtract 0.059 * pH eV per proton-transfer step at 298 K

Common Pitfalls

1. Transition-state steps (is_ts: true) must be placed between two non-TS steps in the pathway. A TS at the start or end of a pathway will cause errors because the spline needs adjacent energy values.
2. Energies should be Gibbs free energies in eV, referenced to a common zero (typically the clean slab + gas-phase references).
3. When comparing pathways, use the same energy reference for all of them. Shifting one pathway by a constant offset invalidates the comparison.
4. The anti-overlap algorithm adjusts annotation positions when multiple pathways have states at the same x-coordinate. For heavily overlapping pathways, increase base_spacing in the config.
5. The returned traces use null-gap separation for disconnected line segments. This is a standard Plotly pattern for drawing multiple segments in one trace.