HEM Agent

Expert agent for Hydroxide Exchange Membrane (HEM) design, Particle Swarm Optimization (PSO), and cation/backbone management.

Table of Contents

• Overview
• Capabilities
• Available Tools
• Workflow
• Example Prompts
• Configuration
• See Also

Overview

The HEM Agent specializes in designing and optimizing cations for Hydroxide Exchange Membranes. It uses Particle Swarm Optimization (PSO) with a Junction Tree VAE to explore the chemical space and find optimal cation structures for specific polymer backbones.

Expertise Areas

• Cation design for anion exchange membranes
• PSO-based molecular optimization
• Backbone structure selection (PBF_BB_1, PP_BB_1, etc.)
• Cation families: tetraalkylammonium, imidazolium, benzimidazolium, guanidinium, piperidinium, spiro_undecane
• HEM properties: alkaline stability, ionic conductivity, water uptake, swelling ratio
• Multi-objective optimization

MCP Server

The HEM Agent connects to the OHMind-HEMDesign MCP server for tool access.

Capabilities

Capability	Description
List Backbones	Enumerate available polymer backbone structures
List Cations	Show available cation families and templates
Validate Config	Check optimization configuration before running
Run Optimization	Execute PSO-based cation optimization
Check Results	Retrieve and display optimization results
Monitor Jobs	View logs from running optimizations
Kill Jobs	Terminate running optimization processes

Available Tools

list_hem_backbones

List available polymer backbones for HEM design.

Returns: List of backbones with SMILES and identifiers

Available Backbones:

• PBF_BB_1, PBF_BB_2 - Polybenzofuran backbones
• PP_BB_1, PP_BB_2, PP_BB_3 - Polyphenylene backbones
• PX_BB_1 - Polyxylene backbone
• PAI_BB_1 - Polyarylimidazolium backbone
• PF_BB_1 - Polyfluorene backbone
• PPO_BB_1, PPO_BB_2, PPO_BB_3 - Polyphenylene oxide backbones

list_cation_types

List available cation families and initial SMILES templates.

Returns: List of cation types with example structures

Available Cations:

• tetraalkylammonium - Quaternary ammonium cations
• imidazolium - Imidazolium-based cations
• benzimidazolium - Benzimidazolium cations
• guanidinium - Guanidinium cations
• piperidinium - Piperidinium cations
• spiro_undecane - Spirocyclic cations

validate_optimization_config

Validate a prospective optimization configuration before running.

Parameters:

• backbone (str): Backbone identifier
• cation_name (str): Cation family name
• property (str): Property mode (multi, ec, ewu, esr)

Returns: Validation result with any issues found

optimize_hem_design

⚠️ EXPENSIVE OPERATION - Requires user approval

Launch PSO-based optimization to design new cation structures.

Parameters:

• backbone (str): Target backbone (e.g., PBF_BB_1)
• cation_name (str): Cation family (e.g., piperidinium)
• property (str): Optimization target
  • multi - Multi-objective (EC, EWU, ESR)
  • ec - Electrical conductivity only
  • ewu - Equilibrium water uptake only
  • esr - Equivalent series resistance only
• num_part (int): Number of particles (default: 250)
• steps (int): Number of PSO steps (default: 5)
• save_path (str, optional): Results directory

Returns: Job status and results location

Estimated Time: 10-15 minutes

check_optimization_results

Check results from completed optimization runs.

Parameters:

• save_path (str): Workspace directory
• backbone (str): Backbone used
• cation_name (str): Cation type used

Returns: Top solutions from CSV logs with SMILES and scores

show_optimization_logs

Stream recent optimization log lines for monitoring.

Parameters:

• backbone (str): Backbone identifier
• cation_name (str): Cation type
• lines (int): Number of lines to show

Returns: Recent log content

kill_optimization_job

List running optimization jobs or terminate one.

Parameters:

• backbone (str, optional): Filter by backbone
• cation_name (str, optional): Filter by cation
• job_id (str, optional): Specific job to kill

Returns: Job status or termination confirmation

Workflow

Standard Optimization Workflow

graph TD
    A[User Request] --> B[List Backbones/Cations]
    B --> C[User Selects Options]
    C --> D[Validate Configuration]
    D --> E{Valid?}
    E --> |No| F[Show Errors]
    F --> C
    E --> |Yes| G[Request Approval]
    G --> H{Approved?}
    H --> |No| I[Cancel]
    H --> |Yes| J[Run Optimization]
    J --> K[Monitor Progress]
    K --> L[Check Results]

Validation Flow

The HEM Agent implements a validation flow for expensive operations:

1. User requests optimization
2. Agent validates configuration
3. Agent displays estimated time and requests approval
4. User approves or cancels
5. If approved, optimization runs

# Validation message format
"⚠️ **HEM Optimization requires approval**

**Configuration:**
- Backbone: `PBF_BB_1`
- Cation: `piperidinium`
- Particles: 250
- Steps: 5
- Results will be saved to: `/OHMind_workspace/HEM`

This is a computationally expensive operation.
Estimated time: 10-15 minutes.

Please approve to continue."

Example Prompts

Discover Design Space

Using your OHMind-HEMDesign tools, list all available backbones and cation 
types, then recommend 2-3 promising backbone-cation combinations for 
alkaline-stable AEMs. Summarize why these combinations are interesting.

Run Multi-Objective Optimization

Design new piperidinium-based cations for backbone PBF_BB_1 optimizing 
multi-objective HEM performance (conductivity, ESR, and water uptake). 
Please run PSO using your default settings and summarize the top 10 candidates.

Check Optimization Results

Show me the results from the PBF_BB_1 piperidinium optimization. 
Display the top 5 candidates with their SMILES and property scores.

Compare Backbones

For backbones PBF_BB_1 and PP_BB_1, design the best tetraalkylammonium 
cations using your HEM optimization tools. Compare the top candidates 
for each backbone in terms of alkaline stability, ESR, and conductivity.

Monitor Running Job

Using your HEMDesign job-management tools, find any currently running 
optimizations. Show me a short snippet of the latest log lines for each job.

Configuration

Environment Variables

Variable	Purpose	Default
HEM_SAVE_PATH	Results storage directory	$OHMind_workspace/HEM
OHMind_workspace	Base workspace path	/OHMind_workspace

Results Storage

Optimization results are saved to:

$HEM_SAVE_PATH/
├── best_solutions_<BACKBONE>_<CATION>.csv
├── best_fitness_history_<BACKBONE>_<CATION>.csv
└── optimization_<BACKBONE>_<CATION>.log

CSV Output Format

The best_solutions_*.csv file contains:

Column	Description
smiles	Optimized cation SMILES
ec_score	Electrical conductivity score
ewu_score	Water uptake score
esr_score	ESR score
fitness	Combined fitness value

See Also

• Agent Reference - Overview of all agents
• HEMDesign MCP Server - Tool documentation
• HEM Optimization Tutorial - Step-by-step guide
• OHPSO Module - PSO implementation details

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Last updated: 2025-12-22 | OHMind v1.0.0