First Steps with OHMind

Learn the basics of interacting with OHMind through practical examples

This guide walks you through your first interactions with OHMind, introducing the main interfaces and basic workflows.

Choosing an Interface
Starting OHMind
Your First Conversation
Understanding Agent Responses
Basic Workflows
Working with Results
Next Steps

Choosing an Interface

OHMind provides three ways to interact with the system:

Interface	Best For	Start Command
CLI (TUI)	Terminal users, quick queries, file preview	`./start_OHMind_cli.sh`
Web UI	Browser-based access, visual workflows	`./start_apps.sh`
API	Programmatic integration, automation	Direct HTTP calls

CLI Features

The terminal user interface (TUI) provides:

Real-time streaming responses
Workspace file browser with preview
Syntax highlighting for code and data files
Export to Markdown, HTML, or SVG
Keyboard shortcuts for efficiency

Web UI Features

The Chainlit-based web interface offers:

Browser-based access from any device
Visual chat profiles for different workflows
MCP server management panel
User authentication and session persistence

Starting OHMind

Option 1: CLI (Recommended for First-Time Users)

cd OHMind
./start_OHMind_cli.sh

The CLI will:

Activate the OHMind conda environment
Set up environment variables
Connect to MCP servers
Display the interactive chat interface

Option 2: Web UI

cd OHMind
./start_apps.sh

Then open http://localhost:8000 in your browser.

Default credentials:

Username: admin
Password: admin

Option 3: Backend Only (for API Access)

cd OHMind
uvicorn app:app --host 0.0.0.0 --port 8005

Your First Conversation

Simple Chemistry Query

Start with a basic chemistry question to verify the system is working:

What is the molecular formula and weight of caffeine?

Expected Response:

The system will:

Route your query to the Chemistry agent
Use the Name2Smiles tool to get caffeine’s SMILES
Calculate molecular properties
Return: C₈H₁₀N₄O₂, ~194.19 g/mol

Understanding the Response

OHMind responses typically include:

Agent identification: Which agent handled your query
Tool calls: What MCP tools were used
Results: The actual answer to your question
Context: Additional relevant information

Understanding Agent Responses

Agent Routing

The Supervisor agent automatically routes queries to specialized agents:

Query Type	Agent	Example
Molecular properties	Chemistry	“What functional groups are in aspirin?”
HEM optimization	HEM	“Design cations for PBF_BB_1 backbone”
QM calculations	QM	“Calculate LUMO energy for this cation”
MD simulations	MD	“Simulate polymer at 400K”
Wavefunction analysis	Multiwfn	“Analyze charge distribution”
Literature search	RAG	“Find papers on alkaline stability”
General web info	Web Search	“Latest research on AEMs”

Tool Execution Indicators

In the CLI, you’ll see visual indicators when tools are executed:

🔧 Calling: MoleculeWeight
   Input: {"smiles": "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"}
   Result: 194.19

Streaming Responses

Both CLI and Web UI support streaming, so you see responses as they’re generated rather than waiting for completion.

Basic Workflows

Workflow 1: Molecular Analysis

Analyze a molecule’s properties and structure:

Analyze the molecule with SMILES "CC(=O)OC1=CC=CC=C1C(=O)O" (aspirin).
Tell me its:
1. Molecular weight and formula
2. Functional groups present
3. A brief description of its structure

What Happens:

Chemistry agent receives the query
Multiple tools are called: MoleculeWeight, Smiles2Formula, FunctionalGroups, MoleculeCaptioner
Results are synthesized into a comprehensive response

Workflow 2: HEM Design Query

Ask about HEM design capabilities:

What backbones and cation types are available for HEM optimization?

What Happens:

HEM agent receives the query
ListBackbones and ListCations tools are called
Available options are presented with descriptions

Workflow 3: Literature Search

Search for relevant scientific literature:

Find recent research on improving alkaline stability of quaternary ammonium cations in AEMs.

What Happens:

RAG agent searches the vector database
Relevant papers and findings are retrieved
A summary of key insights is provided

Workflow 4: Multi-Step Analysis

For complex queries, OHMind creates a task plan:

For the cation SMILES "C[N+]1(C)CCCCC1":
Validate the SMILES
Calculate its molecular properties
Identify functional groups
Suggest potential modifications for improved stability

What Happens:

Supervisor detects a complex query
A task plan is created with multiple steps
Each step is executed in sequence
Results are compiled into a final response

Working with Results

Viewing Generated Files

When OHMind runs calculations, results are saved to the workspace:

In CLI:

Use the sidebar (toggle with Ctrl+B) to browse files
Click on files to preview them
Supports syntax highlighting for code and data files

In Web UI:

Results are displayed inline when possible
File paths are provided for larger outputs

Workspace Structure

Results are organized by domain:

OHMind_workspace/
├── HEM/           # Optimization results
│   ├── best_solutions_*.csv
│   └── optimization_*.log
├── QM/            # QM calculation outputs
│   └── results/
├── MD/            # MD simulation files
│   ├── *.gro
│   └── *.xtc
└── Multiwfn/      # Wavefunction analysis
    └── *.cube

Exporting Conversations

CLI Export Options:

Ctrl+E or /export - Export current conversation
Formats: Markdown, HTML, SVG screenshot

Web UI:

Use the export button in the chat interface

CLI Keyboard Shortcuts

Shortcut	Action
`Ctrl+B`	Toggle workspace sidebar
`Ctrl+L`	Clear chat history
`Ctrl+E`	Export conversation
`Ctrl+C`	Cancel current operation
`Enter`	Send message
`Shift+Enter`	New line in message

Common First-Time Questions

“How do I know which agent is handling my query?”

The response will indicate which agent processed your request. In the CLI, you’ll see agent-specific icons and colors.

“Can I specify which agent to use?”

Yes, you can mention the domain explicitly:

“Using your chemistry tools, analyze…”
“With your HEM optimization capabilities, design…”

“What if a tool fails?”

The system will:

Report the error
Attempt alternative approaches if available
Provide guidance on how to resolve the issue

“How long do calculations take?”

Operation	Typical Time
Molecular properties	< 1 second
HEM optimization (10 steps)	5-15 minutes
QM geometry optimization	10-60 minutes
MD simulation (short)	30+ minutes

Example Session

Here’s a complete example session demonstrating basic usage:

You: What is the molecular weight of benzene?

OHMind: The molecular weight of benzene (SMILES: c1ccccc1) is 78.11 g/mol.

You: Now compare it to toluene - what's the difference?

OHMind: Comparing benzene and toluene:
- Benzene (C₆H₆): 78.11 g/mol
- Toluene (C₇H₈): 92.14 g/mol
- Difference: 14.03 g/mol (one CH₃ group)

Toluene is benzene with a methyl group attached, which accounts for 
the mass difference of approximately one carbon and three hydrogens.

You: What functional groups does toluene have?

OHMind: Toluene contains the following functional groups:
- Aromatic ring (benzene ring)
- Methyl group (alkyl substituent)

The molecule is classified as a methylbenzene or aromatic hydrocarbon.

Next Steps

Now that you’re familiar with basic interactions, explore these topics:

Goal	Resource
Run HEM optimization	HEM Optimization Tutorial
Perform QM calculations	QM Calculations Tutorial
Understand the architecture	Architecture Overview
Learn about agents	Agent Reference
Configure the system	Configuration Guide

First Steps with OHMind

Table of Contents

Choosing an Interface

CLI Features

Web UI Features

Starting OHMind

Option 1: CLI (Recommended for First-Time Users)

Option 2: Web UI

Option 3: Backend Only (for API Access)

Your First Conversation

Simple Chemistry Query

Understanding the Response

Understanding Agent Responses

Agent Routing

Tool Execution Indicators

Streaming Responses

Basic Workflows

Workflow 1: Molecular Analysis

Workflow 2: HEM Design Query

Workflow 3: Literature Search

Workflow 4: Multi-Step Analysis

Working with Results

Viewing Generated Files

Workspace Structure

Exporting Conversations

CLI Keyboard Shortcuts

Common First-Time Questions

“How do I know which agent is handling my query?”

“Can I specify which agent to use?”

“What if a tool fails?”

“How long do calculations take?”

Example Session

Next Steps

See Also