Analysis Modes - Crystalyse v1.0.0¶

Crystalyse v1.0.0 provides three intelligent analysis modes powered by multi-agent orchestration and enhanced UX, allowing you to balance speed, accuracy, and user experience based on your research needs.

Overview¶

Adaptive Mode (Default) - NEW in v1.0.0¶

Purpose¶

Intelligent balance of speed and accuracy with enhanced user experience. Features: - Enhanced Clarification: LLM-powered adaptive questioning based on expertise level - Context-Aware Tool Selection: Automatically chooses optimal tools for each query - Learning Preferences: Adapts behavior based on user patterns and feedback - Workspace Management: Transparent file operations with preview/approval - Intelligent Tool Coordination: Single agent manages specialized tools seamlessly

Enhanced Agent Capabilities¶

Adaptive mode leverages the full feature set of EnhancedCrystaLyseAgent: - Intelligent Tool Selection: Automatically chooses optimal MCP servers and tools - Context-Aware Processing: Adapts responses based on query complexity and user expertise - Workspace Coordination: Manages file operations with transparent preview/approval - Memory Integration: Utilizes session history and discovery cache for informed decisions - Anti-Hallucination Validation: Ensures all numerical results have computational basis

Enhanced UX Features¶

# Adaptive clarification examples:
User: "Find battery materials"
System: "What type of battery application? (Li-ion cathode, Na-ion anode, solid electrolyte, etc.)"

User: "Perovskites for solar cells"  
System: "For single-junction or tandem cells? Any specific efficiency targets?"

Creative Mode¶

Purpose¶

Fast materials exploration with multi-agent coordination. Enhanced in v1.0.0 for: - Initial concept exploration with transparent operations - Rapid prototyping with workspace management - Interactive sessions with real-time progress visualization - Educational demonstrations with adaptive explanations

MCP Server Mapping¶

Creative mode uses the Chemistry Creative Server (chemistry-creative-server):

# Tools available in creative mode
- Chemeleon CSP: Crystal structure prediction
- MACE: Formation energy calculations  
- Visualisation: 3D structure rendering
# Not included: SMACT validation (for speed)

Workflow¶

1. Input: Natural language materials query
2. Structure Generation: Chemeleon generates multiple candidate structures
3. Energy Evaluation: MACE calculates formation energies for ranking
4. Visualisation: Automatic 3D structure files created
5. Output: Ranked structures with energies and interactive visualisations

Example Usage¶

# Command line
crystalyse analyse "Find perovskite solar cell materials" --mode creative

# In unified interface
crystalyse
> /mode creative
> Design high-capacity battery cathodes

# In chat session
crystalyse chat -m creative

Output Structure¶

Creative Mode Results:
├── Structure Generation: 3-5 candidates per composition
├── Energy Ranking: Formation energies (eV/atom)
├── 3D Visualisations: Interactive HTML files
└── Summary: Most stable structures identified

Rigorous Mode¶

Purpose¶

Complete materials validation with specialized agent validation. Enhanced in v1.0.0 for: - Publication-quality research with anti-hallucination safeguards - Detailed materials characterisation with multi-agent cross-validation - Validation of creative/adaptive mode results with specialized agents - Professional materials design projects with comprehensive documentation

MCP Server Mapping¶

Rigorous mode uses the Chemistry Unified Server (chemistry-unified-server):

# Complete tool suite in rigorous mode
- SMACT: Composition validation and screening
- Chemeleon CSP: Crystal structure prediction
- MACE: Formation energy calculations
- Visualisation: 3D structures + analysis plots
- Pymatviz: XRD patterns, RDF analysis, coordination analysis

Workflow¶

1. Input: Natural language materials query
2. Composition Validation: SMACT screens for chemically reasonable compositions
3. Structure Generation: Chemeleon generates structures for valid compositions
4. Energy Evaluation: MACE calculates detailed energetics
5. Comprehensive Analysis: XRD patterns, radial distribution functions, coordination analysis
6. Visualisation: 3D structures + professional analysis plots
7. Output: Complete materials characterisation package

Example Usage¶

# Command line
crystalyse analyse "Validate CsSnI3 for photovoltaic applications" --mode rigorous

# In unified interface
crystalyse
> /mode rigorous
> Analyse LiCoO2 cathode stability

# In chat session
crystalyse chat -m rigorous -s detailed_study

Output Structure¶

Rigorous Mode Results:
├── SMACT Validation: Composition feasibility screening
├── Structure Generation: Multiple candidates with validation
├── Energy Analysis: Formation energies + stability metrics
├── 3D Visualisations: Interactive molecular viewers
├── Analysis Suite:
│   ├── XRD_Pattern_[formula].pdf
│   ├── RDF_Analysis_[formula].pdf
│   ├── Coordination_Analysis_[formula].pdf
│   └── [formula].cif
└── Comprehensive Report: Complete materials characterisation

Mode Switching¶

In Unified Interface¶

crystalyse  # Launch unified interface

# Switch modes during session
> /mode creative    # Fast exploration
> /mode rigorous    # Complete validation

In Chat Sessions¶

crystalyse chat -u researcher -s project_name

# Switch modes within session
🔬 You: /mode rigorous
✅ System: Mode switched to Rigorous
🔬 You: Now analyse the stability in detail

Command Line¶

# Specify mode per analysis
crystalyse analyse "query" --mode creative
crystalyse analyse "query" --mode rigorous

Choosing the Right Mode¶

Use Adaptive Mode When: (Recommended Default)¶

• General research: Most research scenarios benefit from intelligent tool selection
• Learning systems: System adapts to your expertise level and preferences
• Mixed workflows: Combining exploration with validation in one session
• First-time users: Enhanced clarification helps guide effective queries
• Project organization: Workspace management keeps research organized

Use Creative Mode When:¶

• Rapid exploration: Need many quick results for initial screening
• Time-sensitive: Presentations or decision-making with tight deadlines
• Brainstorming: Generating ideas and concepts rapidly
• Educational demos: Quick visual feedback for teaching
• Iterative design: Fast cycles of concept → evaluation → refinement

Use Rigorous Mode When:¶

• Research publications: Need comprehensive validation with cross-checking
• Professional projects: Client work requiring complete documentation
• Critical validation: High-stakes decisions requiring maximum confidence
• Regulatory submissions: Complete traceability and anti-hallucination safeguards
• Deep analysis: Understanding complex materials properties in detail

Performance Characteristics¶

Creative Mode Performance¶

Typical Execution Times:
├── Simple queries: 30-50 seconds
├── Complex materials: 1-2 minutes
├── Multiple compositions: 2-3 minutes
└── Batch analysis: 5-10 minutes

Resource Usage:
├── CPU: Moderate (structure prediction)
├── GPU: Optional (MACE calculations)
├── Memory: 4-6 GB
└── Storage: ~50 MB per analysis

Rigorous Mode Performance¶

Typical Execution Times:
├── Simple queries: 2-3 minutes
├── Complex materials: 3-5 minutes
├── Detailed analysis: 5-10 minutes
└── Batch analysis: 15-30 minutes

Resource Usage:
├── CPU: High (full analysis suite)
├── GPU: Recommended (MACE + visualisation)
├── Memory: 6-8 GB
└── Storage: ~200 MB per analysis

Technical Implementation¶

MCP Server Architecture¶

graph TB
    A[CrystaLyse Agent] --> B{Mode Selection}
    B -->|Creative| C[Chemistry Creative Server]
    B -->|Rigorous| D[Chemistry Unified Server]

    C --> E[Chemeleon CSP]
    C --> F[MACE Energy]
    C --> G[Basic Visualisation]

    D --> H[SMACT Validation]
    D --> I[Chemeleon CSP]
    D --> J[MACE Energy]
    D --> K[Comprehensive Visualisation]
    D --> L[Analysis Suite]

Tool Availability by Mode¶

Best Practices¶

Mode Selection Strategy¶

1. Start with Creative: Use for initial exploration and idea generation
2. Validate with Rigorous: Confirm promising results with complete analysis
3. Iterate: Use creative mode for rapid iteration, rigorous for final validation
4. Match Context: Consider time constraints, audience, and required detail level

Workflow Recommendations¶

# Recommended research workflow
1. Initial Exploration (Creative)
   crystalyse analyse "broad query" --mode creative

2. Focused Investigation (Creative)
   crystalyse chat -m creative
   > Refine based on initial results

3. Detailed Validation (Rigorous)
   crystalyse discover "specific material" --mode rigorous

4. Final Analysis (Rigorous)
   crystalyse chat -m rigorous -s final_study
   > Complete characterisation

Performance Optimisation¶

• Creative Mode: Reduce num_samples for faster iteration
• Rigorous Mode: Use GPU acceleration for MACE calculations
• Both Modes: Enable result caching to avoid redundant calculations
• Batch Processing: Group similar queries for efficiency

Examples¶

Creative Mode Example¶

crystalyse analyse "Design sodium-ion battery cathodes" --mode creative

Output focus: - Quick structure generation (3-5 candidates) - Energy ranking for stability - 3D visualisations for immediate insight - Recommendations for further investigation

Rigorous Mode Example¶

crystalyse discover "Characterise Na2FePO4F cathode material" --mode rigorous

Output focus: - SMACT validation of composition - Multiple structure polymorphs - Detailed energetic analysis - Complete structural characterisation - Professional analysis plots - Publication-ready results

The choice between creative and rigorous modes allows Crystalyse to adapt to your specific research needs, from rapid exploration to comprehensive validation.