Chatmosp Literature Search

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chatmosp-literature-search

1. Core Responsibilities

1. Journal search: access 3 priority layers
2. Article retrieval: 3 stages (abstract → main text → SI)
3. Parameter extraction: extract E_ads, w, gamma from tables
4. Parameter validation: completeness + reasonability + consistency
5. Return scored result to parameter-builder

2. Input Contract

3. Output Contract

Return parameter table (JSON), containing:

⚠️ Literature search does NOT return gas entropy. parameter-builder MUST recalculate it using the §3.1 formula after receiving the result.

4. Workflow

Input (metal + gas)
  → Journal search (3 priority layers)
  → Article retrieval (3 stages: abstract → main text → SI)
  → Parameter extraction (pdftotext + keyword search)
  → Parameter validation (completeness, reasonability, consistency)
  → Output (parameter table with score)

5. Journal Search Priority

Layer 1: Top journals (priority, but may be inaccessible)

• Science, Nature, JACS, Angewandte Chemie, PRL, JCP
• Strategy: DOI resolution → abstract → main text → SI
• API limit or CAPTCHA → immediately skip to Layer 2

Layer 2: Fully open-access journals (recommended)

• Nature Communications
• Science Advances
• PNAS
• ACS Central Science
• Chemical Science

Advantages: completely free, high quality, complete SI

Layer 3: Preprint platforms (last resort)

• arXiv, ChemRxiv, bioRxiv
• Note: not peer-reviewed, parameters may be inaccurate, requires user confirmation

6. Tool Selection

6.1 Prefer the currently available interactive browser/web tool

• ✅ Supports JS rendering
• ✅ Supports login state
• ✅ Supports interactive operations
• ✅ Better suited for journal sites

6.2 Do NOT use web_fetch

• ❌ Journal sites often have restrictions (403, CAPTCHA)
• ❌ Cannot execute JS
• ❌ Cannot get dynamically loaded content

6.3 Fallback

If the current environment has no browser, web-search, PDF, or file-reading tool available, do not pretend that literature retrieval was completed. Ask the user to provide the paper, DOI, SI file, or parameter values directly.

7. Detailed Literature Retrieval Process

Step 1: Build search keywords

✅ Correct format (MUST use):

"keyword1" AND "keyword2" AND "keyword3"

Examples:

• Cu cluster in CO oxidation → "Cu" AND "CO oxidation"
• Pd cluster in CO oxidation → "Pd" AND "CO oxidation"
• Pt cluster in H₂ → "Pt" AND "H2"

❌ Incorrect format (DO NOT use):

Pd CO oxidation

Space-separated format is treated as one keyword, returning inaccurate results.

Step 2: Access journal site

• Use the currently available browser/web tool to enter journal search page
• Input keywords
• Default sort: relevance

Step 3: Get top 10 results

• Only check top 10 (highest relevance)
• Output title, DOI, abstract (optional)

Step 4: Initial screening (by title)

Screening criteria:

1. Reaction atmosphere match (must be target reaction: CO oxidation, WGSR, etc.)
2. Metal system match (must be target metal: Pd, Pt, Cu, etc.; exclude alloys)

Output filtered list + screening reason for each

Step 5: User interaction

Choose next step:

1. Carefully check all filtered articles
2. Carefully check one specific article (user-specified)
3. Switch to another journal

Step 6: Detailed article check

6.1: Check main text

• Confirm metal match
• Confirm reaction atmosphere match
• Look for parameter tables

6.2: No parameters → download SI

• Parameters only exist in text and tables, NOT in images
• Download SI PDF: si_{first_author}_{year}.pdf
• Same author, same year, multiple: si_smith_2023a.pdf / b / c

6.3: Check SI

• Search keywords: Table, Supplementary Table, S1, S2
• Extract parameter tables

Step 7: Parameter extraction

7.1: Download SI via the currently available browser/web tool

7.2: Convert PDF to text

pdftotext si_{author}_{year}.pdf si_{author}_{year}.txt

7.3: Search parameter table keywords

• Table S, Supplementary Table
• adsorption energy, E_ads, binding energy
• surface energy, γ, surface tension
• interaction parameter, interaction matrix

7.4: Use read tool to read text, locate parameter tables

7.5: Extract values from tables, note unit conversions

7.6: Validate parameters

• Within reasonable range
• Follow physical laws
• Consistent

Step 8: Show parameters to user

📊 Parameters extracted from literature:

【Article Information】
- Title: {title}
- DOI: {doi}
- Journal: {journal}

【Parameter Table】
- Surface energy: {values}
- Adsorption energy: {values}
- Interaction matrix: {values}

【Completeness Score】
- Score: {score}/10
- Description: {description}

Please select:
1. ✅ Use these parameters → pass to parameter-builder
2. ❌ Reject, continue searching
3. ❌ Cancel task

8. Article Retrieval 3 Stages

⚠️ IMPORTANT: Main text not mentioning parameters does NOT mean SI lacks them. If article relevance is high, still download SI to check.

9. MSR Required Data Checklist

Basic parameters

• ✅ Metal element, temperature, pressure
• ✅ Cluster radius, gas species, gas partial pressures

Surface parameters (per facet)

• ✅ Surface energy γ (eV/Ų): (100), (110), (111), (211), (311), etc.

Adsorption parameters (per facet + per gas)

• ✅ Adsorption energy E_ads (eV): e.g., CO on Pd(111), O₂ on Pd(100)

Interaction parameters

• ✅ w matrix (eV): CO-CO, CO-O, O-O

Gas parameters

• ✅ Gas entropy (eV/K): can be calculated via formula (T-dependent) or extracted

⚠️ Literature search does NOT return gas entropy; parameter-builder MUST auto-calculate

10. Completeness Scoring

Per-parameter score

Score level action

⚠️ Gas entropy is NOT in this scoring. Regardless of score, parameter-builder MUST recalculate gas entropy per formula.

11. Timeout & Fallback

11.1 Timeout

• Total time limit: 5 minutes
• Per-article limit: 2 minutes
• On timeout: stop immediately, return found parameters (even if incomplete)

11.2 Fallback

After 5 articles without complete parameters:

⚠️ I have searched 5 articles but could not find complete parameters.
- Surface energy: ✅ found
- Adsorption energy: ❌ not found
- Interaction matrix: ❌ not found

Suggestions:
1. Use similar metal as reference
2. Provide known parameter source (DOI or title)
3. Use default/test parameters

11.3 One journal failure prompt

⚠️ No parameters found in top 10 articles of {Journal}

Please select:
1. Switch journal
2. Cancel task (if all journals exhausted, suggest changing system or user-providing params)

12. Lessons Learned

• Lesson 1: Keyword selection
  • Start with broad keywords ("Pd" AND "CO oxidation")
  • Then filter with specific ("adsorption energy")
  • Search topics, not just parameter names
• Lesson 2: DOI priority
  • Prefer known DOI or title
  • Direct DOI access
  • Don't rely solely on keyword search
• Lesson 3: Multi-platform search
  • Don't limit to single journal
  • Prefer open access
• Lesson 4: Don't waste time on inaccessible resources
  • API limit or CAPTCHA → immediately skip to next layer
  • Prioritize open access
• Lesson 5: Main text not mentioning parameters ≠ SI lacks them
  • If article is highly relevant, still download SI
  • SI typically has complete parameter tables

13. Cross-Skill Handoff

• Called by: parameter-builder when key parameters missing + user chooses lit search
• Calls tools: available browser/web/PDF/file-reading tools in the current environment
• Returns to parameter-builder: parameter table with score

14. Dependencies

• chatmosp-parameter-builder — caller
• Browser/web tool — journal site access, SI download
• pdftotext — PDF to text
• read — read text files

15. File Structure

chatmosp-literature-search/
├── SKILL.md       # Chinese reference
└── SKILL_cn.md    # This file (English)

16. Practical Example

User: show me the Pd cluster under atmosphere of CO and O2

1. Extract need: metal=Pd, gases=[CO, O₂]
2. Check MOSP_database: no match
3. parameter-builder prompts with 4 options → user chooses literature search (open access)
4. Launch this skill:
   - Platform: Nature Communications
   - Keywords: `"Pd" AND "CO oxidation" AND "adsorption energy"`
   - Tool: currently available browser/web tool
5. Find relevant article, confirm DOI
6. Download SI → save to literature/
7. pdftotext → search "Supplementary Table" → extract parameters
8. Validate: completeness score
9. Display result + annotate missing
10. User confirms → pass to parameter-builder to assemble input.json

Key points:
- Always start with open-access journals
- Literature search does NOT return gas entropy; parameter-builder MUST recalculate
- Interaction parameters may be in KMC format; need MSR/KMC format conversion (see parameter-builder §9)

ChatMOSP Companion Skills

This skill is part of the ChatMOSP skill set. For complete functionality, install the companion ChatMOSP skills from ClawHub when they are missing:

• chatmosp-input-coordinator
• chatmosp-parameter-builder
• chatmosp-msr-generator
• chatmosp-kmc-simulator
• chatmosp-literature-search
• chatmosp-file-organizer

If a required companion skill is unavailable, ask the user to install the missing ChatMOSP skill from ClawHub before continuing. Use the GitHub repository only as a fallback.